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  • R + Bioconductor : combining probesets in an ExpressionSet

    - by Mike Dewar
    Hi, First off, this may be the wrong Forum for this question, as it's pretty darn R+Bioconductor specific. Here's what I have: library('GEOquery') GDS = getGEO('GDS785') cd4T = GDS2eSet(GDS) cd4T <- cd4T[!fData(cd4T)$symbol == "",] Now cd4T is an ExpressionSet object which wraps a big matrix with 19794 rows (probesets) and 15 columns (samples). The final line gets rid of all probesets that do not have corresponding gene symbols. Now the trouble is that most genes in this set are assigned to more than one probeset. You can see this by doing gene_symbols = factor(fData(cd4T)$Gene.symbol) length(gene_symbols)-length(levels(gene_symbols)) [1] 6897 So only 6897 of my 19794 probesets have unique probeset - gene mappings. I'd like to somehow combine the expression levels of each probeset associated with each gene. I don't care much about the actual probe id for each probe. I'd like very much to end up with an ExpressionSet containing the merged information as all of my downstream analysis is designed to work with this class. I think I can write some code that will do this by hand, and make a new expression set from scratch. However, I'm assuming this can't be a new problem and that code exists to do it, using a statistically sound method to combine the gene expression levels. I'm guessing there's a proper name for this also but my googles aren't showing up much of use. Can anyone help?

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  • Cocoa - array not sorting?

    - by Mike
    I have this set NSMutableSet *mySet = [NSMutableSet setWithObjects: @"2", @"8", @"7", @"0", @"3", nil]; I copy the set to an array and sort it using NSArray *sortedArray = [[mySet allObjects] sortedArrayUsingSelector:@selector(compare:)]; The resulting array is in exactly the same order as the set and is not being sorted. Why? thanks for any help. EDIT: CORRECING A TYPO.

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  • What's it like being a financial programmer?

    - by Mike
    As a student who's done an internship at a Silicon Valley company(non-financial), I'm curious to know what it's like working for a financial company doing software development. I'd expect the hours to be longer, and the pay to be higher. Specifically, I have the following questions: What's the work/life balance really like? Are you expected to work 80 hours a week most weeks? For those who have worked in non-financial software engineering jobs, how does being a financial software engineer compare in terms of work/life balance? How much does it pay? I'm curious as to starting(i.e. just got a BS) pay, as well as "top out" pay. (I'd prefer concrete numbers - ballpark is fine). Also, bonuses would be useful information. What jobs do financial programmers typically have? Are most just general software engineers, or do people typically have very specialized(i.e. AI or systems) backgrounds? Also, do most programmers have PhDs? Are programmers typically required to be at work, or are financial companies generally flexible about letting programmers work from home? When at work, do programmers have to dress formally? What are the technology environments like? Are finance companies using state-of-the-art hardware and software, or are they generally more conservative in upgrading their equipment? What programming languages are typically used? If VBA(shudder) is used, is it a large part of a finance company's workflow? If you could turn back the clock, would you still be a financial programmer? I'm going to keep this post open a little bit longer to get some more responses.

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  • IIS7 and 301 permanment redirects using the location tag in web.config (ASP.NET MVC application)

    - by Mike
    I need to setup some 301 permanent redirects in the web.config of an ASP.NET MVC application running under IIS. The easiest way is to add a tag similar to the one below to the web.config file: <location path="TheMenu.aspx"> <system.webServer> <httpRedirect enabled="true" destination="menus/" httpResponseStatus="Permanent" /> </system.webServer> </location> When I go to the site at http://domain.com/TheMenu.aspx it redirects me to http://domain.com/menusxd instead of http://domain.com/menus What would be causing this? Thanks!

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  • portlet-mvc 3.0 + maven for websphere portlet: examples?

    - by Mike
    I'm trying to develop a websphere portal portlet using java, maven and spring-portlet-mvc 3.0.2.RELEASE but so far I'm not having a lot of luck. The problem that I'm having is that a lot of the tutorials are either outdated, incorrect, contradict eachother or a combination of all the above. Also I have to use RAD but the tutorials also contradict eachother, logically I'd think you'd choose new portlet project, but http://www.ibm.com/developerworks/websphere/library/techarticles/0802_patil-pt1/0802_patil-pt1.html says to use a dynamic webproject. So I was wondering if anyone had a nice example/good tutorial.

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  • Maddening Linked List problem

    - by Mike
    This has been plaguing me for weeks. It's something really simple, I know it. Every time I print a singly linked list, it prints an address at the end of the list. #include <iostream> using namespace std; struct node { int info; node *link; }; node *before(node *head); node *after(node *head); void middle(node *head, node *ptr); void reversep(node *head, node *ptr); node *head, *ptr, *newnode; int main() { head = NULL; ptr = NULL; newnode = new node; head = newnode; for(int c1=1;c1<11;c1++) { newnode->info = c1; ptr = newnode; newnode = new node; ptr->link = newnode; ptr = ptr->link; } ptr->link=NULL; head = before(head); head = after(head); middle(head, ptr); //reversep(head, ptr); ptr = head; cout<<ptr->info<<endl; while(ptr->link!=NULL) { ptr=ptr->link; cout<<ptr->info<<endl; } system("Pause"); return 0; } node *before(node *head) { node *befnode; befnode = new node; cout<<"What should go before the list?"<<endl; cin>>befnode->info; befnode->link = head; head = befnode; return head; } node *after(node *head) { node *afnode, *ptr2; afnode = new node; ptr2 = head; cout<<"What should go after the list?"<<endl; cin>>afnode->info; ptr2 = afnode; afnode->link=NULL; ptr2 = head; return ptr2; } void middle(node *head, node *ptr) { int c1 = 0, c2 = 0; node *temp, *midnode; ptr = head; while(ptr->link->link!=NULL) { ptr=ptr->link; c1++; } c1/=2; c1-=1; ptr = head; while(c2<c1) { ptr=ptr->link; c2++; } midnode = new node; cout<<"What should go in the middle of the list?"<<endl; cin>>midnode->info; cout<<endl; temp=ptr->link; ptr->link=midnode; midnode->link=temp; } void reversep(node *head, node *ptr) { node *last, *ptr2; ptr=head; ptr2=head; while(ptr->link!=NULL) ptr = ptr->link; last = ptr; cout<<last->info; while(ptr!=head) { while(ptr2->link!=ptr) ptr2=ptr2->link; ptr = ptr2; cout<<ptr->info; } } I'll admit that this is class work, but even the professor can't figure it out, and says that its probably something insignificant that we're overlooking, but I can't put my mind to rest until I find out what it is.

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  • Setting Parameters from another Parameter In SSRS

    - by Mike
    I was able to get this working is SSRS 2008, but do to the fact that my company only has 2005 servers I need to downgrade the report to 2005. The idea is for a given person name there are two key fields EntityType and EntityId So I have a parameter from a dataset where the Label is the Name and the value is EntityType_EntityId I use the split function to take the left and right sides of from _ In 2008, I set the query parameters of the dataset to the split function and it works In 2005, I set the Default Value of each Report Parameters Now when I run the report and put textboxes showing the value of the parameters, the values are shown correctly but the query does not run. I am guessing that this is a lifecycle issue being Get Name Parameter Run Report THEN Set Parameters = Split of Name But the problem with that is the second time I run the report I should get result and I do not. Does anyone know what I am doing wrong. I guess I can pass in the underscore delimted string to the stored procedure and parse it there, but my question is can this be done in the report? Reason being other callers will pass in the parameters as two seperate values.

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  • How to retrieve an array from Multidimensional Array.

    - by Mike Smith
    So I have a multi-dimensional array looks like this. $config = array( "First Name" => array( "user" => $_POST['firstname'], "limit" => 35, ), "Last Name" => array( "user" => $_POST['lastname'], "limit" => 40, ), ); I want use the array that's within the config array, so my approach is to use a foreach loop. foreach($config as $field => $data) { } Now I know that $data will be my array, but it seems I can't use it outside of the foreach statement because I only get half of whats already there. Using print_r you can see what it shows outside the loop: Array ( [user] => lastname [limit] => 40 ) But when inside the loop and I use print_r here is my result: Array ( [user] => firstname [limit] => 35 ) Array ( [user] => lastname [limit] => 40 ) I imagine it has to do something with it being with the foreach loop. I've tried to run a foreach on the $data array to populate another array, but that didn't work as well. Is there a way to use this outside of a foreach loop? Sorry if this a dumb question, I'm sure there is a quite a simple answer to this, but I'm just stumped, and can't think of a way to do this. Thanks.

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  • Perl, print with newline

    - by Mike
    In perl most of my print statements take the form print "hello." . "\n"; Is there a nice way to avoid keeping all the pesky "\n"s lying around? I know I could make a new function such as myprint that automatically appends \n, but it would be nice if I could override the existing print.

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  • Core Data ANY BETWEEN predicate

    - by Mike Weller
    I'm trying to create an NSPredicate to find 'projects' that contain 'sessions' within a certain date range. I tried this at first: [NSPredicate predicateWithFormat:@"ANY sessions.date BETWEEN {$STARTDATE, $ENDDATE}"]; But I get an exception: *** Terminating app due to uncaught exception 'NSInvalidArgumentException', reason: 'to-many key not allowed here' It seems BETWEEN does not work with ANY in this way. I'm also limited in use of () and AND clauses meaning I can't use something like: [NSPredicate predicateWithFormat:@"ANY (sessions.date > $STARTDATE && sessions.date < $ENDDATE)"]; If I try that I get a parse error. How can I do this? Thanks UPDATE: Note that this: [NSPredicate predicateWithFormat:@"ANY sessions.date > $STARTDATE && ANY sessions.date < $ENDDATE"]; Is incorrect because it returns a project where there is a session greater than the start date and another session less than the end date but no session in between.

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  • Experienced developer trying to get outsourcing contract with current client.

    - by Mike
    I work for a major bank as a contract software developer. I've been there a few months, and without exception this place has the worst software practices I've ever seen. The software my team makes has no formal testing, terrible code (not reusable, hard to read, etc), minimal documentation, no defined development process and an absolutely sickening amount of waste due to bureaucratic overhead. Part of my contract is to maintain a group of thousands of very poorly written batch jobs. When one of the jobs fails (read: crashes), it's a developers job to look at the source, figure out what's wrong, fix it, and check it in. There is no quality assurance process or auditing of the results whatsoever. Once the developer says "it works" a manager signs off and it goes into production. What's disturbing is that these jobs essentially grab market data and put it into a third-party risk management system, which provides the bank with critical intelligence. I've discovered the disturbing truth that this has been happening since the 90s and nobody really has evidence the system is getting the correct data! Without going into details, an issue arose on Friday that was so horrible I actually stormed out of the place. I was ready to quit, but I decided to just get out to calm my nerves and possibly go back Monday. I've been reflecting today on how to handle this. I have realized that, in probably less than 6 months, I could (with 2 other developers) remake a large component of this system. The new system would provide them with, as primary benefits, a maintainable codebase less prone to error and a solid QA framework. To do it properly I would have to be outside the bank, the internal bureaucracy is just too much. And moreover, I think a bank is fundamentally not a place that can make good software. This is my plan. Write a report explaining in depth all the problems with their current system Explain why their software practices fail and generate a tremendous amount of error and waste. Use this as the basis for claiming the project must be developed externally. Write a high level development plan, including what resources I will require Hand 1,2,3 to my manager, hopefully he passes it up the chain. Worst case he fires me, but this isn't so bad. Convinced Executive decides to award my company a contract for the new system I have 8 years experience as a software contractor and have delivered my share of successful software products, but all working in-house for small/medium sized companies. When I read this over, I think I have a dynamite plan. But since this is the first time doing something this bold so I have my doubts. My question is, is this a good idea? If you think not, please spare no detail.

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  • iphone - compiler conditional on header

    - by Mike
    I have a project that generates applications for two targets. One of the targets has to include one additional delegate protocol that should not be present on the other one. So, I have created a macro on Xcode and declared the header like this: #ifdef TARGET_1 @interface myViewController : UIViewController <UIScrollViewDelegate, UIPopoverControllerDelegate> #endif #ifdef TARGET_2 @interface myViewController : UIViewController <UIScrollViewDelegate> #endif { .... bla bla.... } The problem is that Xcode is not liking this "double" declaration of @interface and is giving me all sort of problems. How to solve that? thanks for any help.

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  • Oversized Qt Fonts on OSX

    - by Mike Arthur
    Why does Qt on OSX appear to default to overly large fonts? Even when you select the same font size manually the fonts appear slightly bigger. Does Qt on OSX use a different font rendering to OSX? Does this improve if you use Qt for Cocoa? In addition, is there a qtconfig tool or equivalent to globally set the font settings for all Qt applications? Thanks!

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  • spring add default value to form:select

    - by Mike
    I'm developing a spring application, now I've added a dropdownlist to one of my jsp pages using: <form:select multiple="single" path="users[y.count-1].X" items="${Y}" itemValue="id" itemLabel="name"/> Now I'd like to add the default value "Nothing selected", however I can't seem to find how to do this. I've tried: <form:select multiple="single" path="users[y.count-1].X" items="${Y}" itemValue="id" itemLabel="name"> <form:option value="Nothing selected" /> </form:select> But "Nothing selected" isn't displayed in my dropdownlist.

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  • NSMutableUrlRequest eats plus signs

    - by Mike
    I create NSMutableUrlRequest for sending data to server, add all necessary fields to it and then add the string for sending like this: [theRequest setHTTPBody:[postString dataUsingEncoding: NSUTF8StringEncoding]]; postString is a usual NSString. The problem is, when I receive this request at the server, all the plus (+) signs disappear from the http body. So if I had "abcde+fghj" on iPhone, I get "abcde fghj" on the server". Can this be some encoding problem from using dataUsingEncoding: NSUTF8StringEncoding? Or some NSMutableUrlRequest stripping feature? What can I do to make it stop stripping plus signs? I need to receive UTF8 strings at the server side.

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  • How can I set up .Net unhanlded exception handling in a windows service?

    - by Mike Pateras
    protected override void OnStart(string[] args) { AppDomain.CurrentDomain.UnhandledException += new UnhandledExceptionEventHandler(CurrentDomain_UnhandledException); Thread.Sleep(10000); throw new Exception(); } void CurrentDomain_UnhandledException(object sender, UnhandledExceptionEventArgs e) { } I attached a debugger to the above code in my windows service, setting a breakpoint in CurrentDomain_UnhandledException, but it was never hit. The exception pops up saying that it is unhandled, and then the service stops. I even tried putting some code in the event handler, in case it was getting optimized away. Is this not the proper way to set up unhandled exception handling in a windows service?

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  • What do you use to keep notes as a developer?

    - by Mike Duncan
    Where as a developer do like to you keep your code snippets, links, checklists, final solutions to problems etc? I've fooled with Google Notebook, MS Onenote, TreePad, textfiles, and Evernote a bit (currently leaning toward Evernote). All have pros and cons but none seem to be really suited to developers. Is anyone super-happy with a collection / note system that's not just generic GTD, but with developer-centric utility?

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  • Perl, share package variable without Export

    - by Mike
    I'm creating a group of Perl scripts, and I would like to have one package store a group of constants. I don't want to export them using Exporter because there will be quite a few and I don't want to pollute the namespace. Since there will be so many, I don't want to require the user to be forced to manually specify which they will be using. I think the best way to just use the packagename::var syntax, however it doesn't seem to be working as I expect it to. I illustrate this problem in the below code This is settings.pm, the module that will hold the global settings #!/usr/bin/perl #settings.pm use strict; use warnings; package settings; our $foo="hello world"; 1; Below is the main script #!/usr/bin/perl #script.pl use strict; use warnings; use settings; print settings::$foo; It gives this error message instead or printing hello world Bad name after settings:: at ./script.pl line 8.

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  • Batch Geocoding with Garmin Mapsource

    - by Mike Trader
    Please Note: I AM NOT LOOKING FOR AN ALTERNATIVE SOLUTION I lost track of this effort years ago but have need to geocode thousands of addresses nightly. I must use the very accurate database sitting on the machine, installed when the Nuvi map update installed Mapsource. When I contacted Garmin years ago, they expressed an interest in providing an API for this, but then I heard nothing and did not follow up. Their database is provided by navtec? I believe. Anyone have experience with that format? I posted on the Garmin Developer forum a while ago, but its a little lethargic over there :) Has anyone done this? Does anyone know how it might be done without an API; meaning database structure and calls? I'll take a solution in any language. Added: Garmin has expressed an interest in making this available to me. They just have not done it. I do not know the database format. I am NOT looking for an online solution or any other "alternative". This question is very specific. Contact Info: MikeTrader2 A T gmail D O T com Added: I offered a 400 pt bounty for this. Jeff Atwood then offered 400pts also. If you would like to see a solution to this, vote up the question and I will chase up Garmin and show there is interest in finally providing this. Please Note: I AM NOT LOOKING FOR AN ALTERNATIVE SOLUTION

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  • accepts_nested_attributes_for ignore blank values

    - by Mike
    i have class Profile has_many :favorite_books, :dependent => :destroy has_many :favorite_quotes, :dependent => :destroy accepts_nested_attributes_for :favorite_books, :allow_destroy => true accepts_nested_attributes_for :favorite_quotes, :allow_destroy => true end I have a dynamic form where you press '+' to add new textareas for creating new favorites. What i want to do is ignore the blank ones, I find this harder to sort through in the update controller than a non nested attribute. What i have temporarily is a hack in the after_save callback deleting the empty records. Whats the most rails way to ignore these blank objects? I dont want validation and errors, just a silent deletion/ignore.

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  • Eclipse code template to insert a bookmark?

    - by Mike
    Eclipse has a nifty feature which allows you to define "templates" for code. I have created one to automatically put in a println and add a "TODO" comment. I'd like for this to also add a bookmark so I can easily find it again. (The codebase I am working with makes it unfeasible to use just the Task List to find what I need to do since there are a lot of TODOs laying around.) My current template is simply System.out.println("don't commit me!"); //TODO: fix this ${cursor}.

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  • In Perl, is a while loop generally faster than a for loop?

    - by Mike
    I've done a small experiment as will be shown below and it looks like that a while loop is faster than a for loop in Perl. But since the experiment was rather crude, and the subject might be a lot more complicated than it seems, I'd like to hear what you have to say about this. Thanks as always for any comments/suggestions :) In the following two small scripts, I've tried while and for loops separately to calcaulte the factorial of 100,000. The one that has the while loop took 57 minutes 17 seconds to finish while the for loop equivalent took 1 hour 7 minutes 54 seconds. Script that has while loop: use strict; use warnings; use bigint; my $now = time; my $n =shift; my $s=1; while(1){ $s *=$n; $n--; last if $n==2; } print $s*$n; $now = time - $now; printf("\n\nTotal running time: %02d:%02d:%02d\n\n", int($now / 3600), int(($now % 3600) / 60), int($now % 60)); Script that has for loop: use strict; use warnings; use bigint; my $now = time; my $n =shift; my $s=1; for (my $i=2; $i<=$n;$i++) { $s = $s*$i; } print $s; $now = time - $now; printf("\n\nTotal running time: %02d:%02d:%02d\n\n", int($now / 3600), int(($now % 3600) / 60), int($now % 60));

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  • Favorite Drupal tips or best practices?

    - by Mike Crittenden
    Just wondering what tips or tricks you guys might have to share. As always with posts like this, please only one tip per post so they can be voted on independently. I'll start: however you do your theming, you can use the mothership theme as a base theme for your theme to inherit from so that your markup will be a lot cleaner and less verbose.

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