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  • hierarchical clustering with gene expression matrix in python

    - by user248237
    how can I do a hierarchical clustering (in this case for gene expression data) in Python in a way that shows the matrix of gene expression values along with the dendrogram? What I mean is like the example here: http://www.mathworks.cn/access/helpdesk/help/toolbox/bioinfo/ug/a1060813239b1.html shown after bullet point 6 (Figure 1), where the dendrogram is plotted to the left of the gene expression matrix, where the rows have been reordered to reflect the clustering. How can I do this in Python using numpy/scipy or other tools? Also, is it computationally practical to do this with a matrix of about 11,000 genes, using euclidean distance as a metric? thanks.

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  • Can't print elements in a DIV tag

    - by Mckenzi
    I am using a Drag-able and re-sizeable DIV's in this HTML file. Where the user will place the DIV tag to his desired place in a main parent DIV tag. Now I want to print this main DIV tag, but the problem is that the code which I'm using to PRINT this main DIV is printing in a sequence, like not the way user has arranged the DIV's. Also it doesn't take up the main DIV background IMAGE. here is the code. JAVASCRIPT & CSS <link rel="stylesheet" type="text/css" href="byrei-dyndiv_0.5.css"> <script type="text/javascript" src="http://jqueryjs.googlecode.com/files/jquery-1.3.1.min.js" > </script> <script type="text/javascript" src="byrei-dyndiv_1.0rc1.js"></script> <script language="javascript" type="text/javascript"> function change(boxid,divtoaffect) { content = document.getElementById("" + boxid + "").value.replace(/\n/g, '<br>'); document.getElementById(divtoaffect).innerHTML = content; } function select1() { test=document.getElementById("changeMe"); test.style.backgroundImage="url('Sunset.jpg')"; } function select2() { test=document.getElementById("changeMe"); test.style.backgroundImage="url('Blue hills.jpg')"; } function PrintElem(elem) { Popup($(elem).text()); } function Popup(data) { var mywindow = window.open('', 'my div', 'height=400,width=600'); mywindow.document.write('<html><head><title>my div</title>'); /*optional stylesheet*/ //mywindow.document.write('<link rel="stylesheet" href="main.css" type="text/css" />'); mywindow.document.write('</head><body >'); mywindow.document.write(data); mywindow.document.write('</body></html>'); mywindow.document.close(); mywindow.print(); return true; } // Print DIV function printContent(id){ str=document.getElementById(id).innerHTML newwin=window.open('','printwin','left=100,top=100,width=400,height=400') newwin.document.write('<HTML>\n<HEAD>\n') newwin.document.write('<TITLE>Print Page</TITLE>\n') newwin.document.write('<script>\n') newwin.document.write('function chkstate(){\n') newwin.document.write('if(document.readyState=="complete"){\n') newwin.document.write('window.close()\n') newwin.document.write('}\n') newwin.document.write('else{\n') newwin.document.write('setTimeout("chkstate()",2000)\n') newwin.document.write('}\n') newwin.document.write('}\n') newwin.document.write('function print_win(){\n') newwin.document.write('window.print();\n') newwin.document.write('chkstate();\n') newwin.document.write('}\n') newwin.document.write('<\/script>\n') newwin.document.write('</HEAD>\n') newwin.document.write('<BODY onload="print_win()">\n') newwin.document.write(str) newwin.document.write('</BODY>\n') newwin.document.write('</HTML>\n') newwin.document.close() } </script> </head> <body> <style type="text/css"> #output1,#output2 ,#output3 { width: 300px; word-wrap: break-word; border: solid 1px black; } </style> HTML <div style="width:650px;height:300px;" id="changeMe" > <table cellpadding="5" cellspacing="0" width="100%" style="margin:auto;"> <tr> <td><div class="dynDiv_moveDiv" id="output1" style="font-weight:bold;height:20px;margin-top:40px;"> <div class="dynDiv_resizeDiv_tl"></div> <div class="dynDiv_resizeDiv_tr"></div> <div class="dynDiv_resizeDiv_bl"></div> <div class="dynDiv_resizeDiv_br"></div> </div> </td> </tr> <tr> <td><div class="dynDiv_moveDiv" id="output2" style="height:40px;margin-top:30px;"> <div class="dynDiv_resizeDiv_tl"></div> <div class="dynDiv_resizeDiv_tr"></div> <div class="dynDiv_resizeDiv_bl"></div> <div class="dynDiv_resizeDiv_br"></div> </div></td> </tr> <tr> <td><div class="dynDiv_moveDiv" id="output3" style="height:50px;margin-top:40px;"> <div class="dynDiv_resizeDiv_tl"></div> <div class="dynDiv_resizeDiv_tr"></div> <div class="dynDiv_resizeDiv_bl"></div> <div class="dynDiv_resizeDiv_br"></div> </div></td> </tr> </table> </div> <tr> <td align="center"><input type="button" value="Print Div" onClick="printContent('changeMe')" /> </td> </tr>

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  • Regular expression only for website

    - by Katie
    HI, I'm new to Regular Expression. I need to find just website in some text and I'm looking for a regular expression able to find out strings like: www.my.home, http://my.site.it But this regular expression should not find strings like: [email protected] or if the website is already inside html tag <a href="http://www.my.site.com/"><span style="font-style: normal;">www.mambo-test.org</span></a> I tried with this one: \b((https?://[^ ])|(www.[^ ])) but it also finds the website in the href and between the tag: <a href="http://www.my.site.com/"><span style="font-style: normal;">www.mambo-test.org</span></a> and I don't know how except this case.

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  • Expression.Call() to String.Equals() throws error

    - by Sam
    The following code: var constant = Expression.Constant("find me", typeof(string)); // memberExpression evaluates to a string var predicate = Expression.Call(memberExpression, "Equals", null, constant); is throwing the error More than one method 'Equals' on type 'System.String' is compatible with the supplied arguments. I'm guessing that's because there's Equals(Object) and Equals(String) - is there any way for me to specify which method I mean to use via the overload of Expression.Call() that takes an instance method name as a string? Or do I have to make a special case for calls to Equals() to take a MethodInfo instead?

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  • Custom Expression in Linq-to-Sql Designer

    - by csharpnoob
    According to Microsoft: http://msdn.microsoft.com/de-de/library/system.data.linq.mapping.columnattribute.expression.aspx It's possible to add expression to the Linq-to-SQL Mapping. But how to configure or add them in Visual Studio in the Designer? Problem, when I add it manual to thex XYZ.designer.cs it on change it will be lost. //------------------------------------------------------------------------------ // <auto-generated> // This code was generated by a tool. // Runtime Version:2.0.50727.4927 // // Changes to this file may cause incorrect behavior and will be lost if // the code is regenerated. // </auto-generated> //------------------------------------------------------------------------------ This is generated: [Column(Name="id", Storage="_id", DbType="Int")] public System.Nullable<int> id { ... But i need something like this [Column(Name="id", Storage="_id", DbType="Int", Expression="Max(id)")] public System.Nullable<int> id { ... Thanks.

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  • whats wrong with this regular expression c#?

    - by Greezer
    I runned into a problem with my regular expressions, I'm using regular expressions for obtaining data from the string below: "# DO NOT EDIT THIS MAIL BY HAND #\r\n\r\n[Feedback]:hallo\r\n\r\n# DO NOT EDIT THIS MAIL BY HAND #\r\n\r\n" So far is got it working with: String sFeedback = Regex.Match(Message, @"\[Feedback\]\:(?<string>.*?)\r\n\r\t\n# DO NOT EDIT THIS MAIL BY HAND #").Groups[1].Value; This works except if the header is changed, therefore I want the regex to read from [feedback]: to the end of the string. (symbols, ascii, everything..) I tried: \[Feedback]:(?<string>.*?)$ Above regular expression does work in some regular expression builders online but in my c# code its not working and returns a empty string. can someone help me with this regular expression? thanks in advance

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  • "Cannot use fixed local inside lambda expression"

    - by JulianR
    I have an XNA 3.0 project that compiled just fine in VS2008, but that gives compile errors in VS2010 (with XNA 4.0 CTP). The error: Cannot use fixed local 'depthPtr' inside an anonymous method, lambda expression, or query expression depthPtr is a fixed float* into an array, that is used inside a Parallel.For lambda expression from System.Threading. As I said, this compiled and ran just fine on VS2008, but it does not on VS2010, even when targeting .NET 3.5. Has this changed in .NET 4.0, and even so, shouldn't it still compile when I choose .NET 3.5 as the target framework? Searching for the term "Cannot use fixed local" yields exactly one (useless) result, both in Google and Bing. If this has changed, what is the reason for this? I can imagine capturing a fixed pointer-type in a closure could get a bit weird, is that why? So I'm guessing this is bad practice? And before anyone asks: no, the use of pointers is not absolutely critical here. I would still like to know though :)

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  • asp.net regular expression not working as expected

    - by Zaps
    Hi, I have a textbox and a regular expression validator applied to it. I want to make sure that the only allowed string inputted into the textbox are "Anything Entered" or "Something Else" or "Another String" otherwise I want an error to be displayed. This is the regular expression I have so far: ValidationExpression="(^Anything Entered)$|(^Something Else)$ |(^Another String)$" However when I enter the supposed valid strings the error is displayed. I cant figure out whats wrong with the expression. Any help would be greatly appreciated. Thanks, Zaps

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  • regular expression

    - by Altariste
    Hi, I need to find all invocations of some logging macros in the code. The macro invocation is of the form: DEBUG[1-5] ( "methodName: the logged message", arguments) But the new versions of the macros are prepending the name of the method automatically, so my task is to write a Python script that will remove the duplicate function names specified already by the programmer. I'm using the sub function from the re module. I plan to substitute the part indicated by || signs below : ||DEBUG[1-5] ("methodName: || the logged message", arguments) with simply DEBUG[1-5](" The problem is following: To find the expressions I want to substitute, I use the following regular expression: ((DEBUG | INFO | all other macros names )[1-5]*)\s*\(\"\w+: But it doesn't match the whole expression ( from DEBUG right to the colon ), but only the macro name, that is for example DEBUG5. Is my expression wrong or there is some quirk in the Python regex processing? ( maybe the fact that I use the DEBUG[1-5] as a subgroup has something to do with this? ) Help from anyone more knowledgable than me appreciated :).

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  • Search outlook 2003 using a regular expression

    - by Doug T.
    Every week I have to do the same report for my bosses. Our bug tracker sends us emails, and to be sure I caught everything I often need to search Outlook for all the bug email's I've received. If I could search the email subject using a regular exrpession, my life would be much easier. Can I search my inbox using a regular expression in Outlook 2003?

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  • I am trying to use user-defined functions to print out an inputted letter out of stars, but i need h

    - by lm
    def horizline(col): for col in range (col): print("*", end='') print() def vertline(rows, col): for rows in range (rows-2): print ("*", end='') for col in range (col-2): print(' ', end='') print("*") def functionA(width): horizline(width) vereline(width) horizline(width) vertline(width) print() #def funtionB(width): #def functionC(width): #def functionE(width): def main(): width=int(input("Please enter a width for the letter: ")) lenght=int(input("Please enter a lenght for the letter: ")) letter=input("Enter one of the capital letters: A,B,C,E ") if(width>=5 and width<=20): functionA functionB(width,length) functionC(width,length) functionE(width,length) else: print("You have entered an incorrect value") main()

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  • I am trying to use user-defined functions to print out an A out of stars, but i need help defining m

    - by lm
    def horizline(col): for col in range (col): print("*", end='') print() def vertline(rows, col): for rows in range (rows-2): print ("*", end='') for col in range (col-2): print(' ', end='') print("*") def functionA(width): horizline(width) vertline(width) horizline(width) vertline(width) print() def main(): width=int(input("Please enter a width for the letter: ")) length=int(input("Please enter a lenght for the letter: ")) letter=input("Enter one of the capital letters: A ") if(width>=5 and width<=20): functionA(width) else: print("You have entered an incorrect value") main()

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  • I am trying to use user-defined functions to print out an T out of stars, but i need help shifting t

    - by lm
    I know main() and other parts of the prog are missing, but please help def horizLine(col): for cols in range(col): print("*", end='') print() def line(col): #C,E,F,G,I,L,P,T for col in range(col//2): print("*", end='') print() def functionT(width): horizLine(width) line(width) enter width for the box width = int(input("Enter a width between 5 and 20: ")) letter=input("Enter one of the capital letters: T ") if ((width >= 5 and width <=20)): if letter=="T": functionT(width) else: print() print("Invalid letter!") else: print("You have entered a wrong range for the width!") main()

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  • Error when connecting to shared Windows Printers

    - by TrueDuality
    I'm replacing our Windows 2003 print server with one running on Windows 2008 R2. I have connected and configured all of our printers and can successfully print to them from the server itself. All of the printers are shared and user's have permission to print on all of them. Whenever one of our clients attempts to connect through the shares they receive the following error message: Operation could not be completed (error 0x0000709). Double check the printer name and make sure that the printer is connected to the network. No messages are generated on the client Event Log nor is anything generated on the server. I have reinstalled the drivers as suggested by a few forum posts I came across and it didn't solve the issue. There are twelve different printer drivers and they are all experiencing this issue so I believe it is unrelated to the driver. I have disabled UAC on both the client and server since that has caused so many headaches before, but it too did not solve this problem. Does anyone have any idea what may be causing this?

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  • RegexClean Transformation

    Use the power of regular expressions to cleanse your data right there inside the Data Flow. This transformation includes a full user interface for simple configuration, as well as advanced features such as error output configuration. Two regular expressions are used, a match expression and a replace expression. The transformation is designed around the named capture groups or match groups, and even supports multiple expressions. This allows for rich and complex expressions to be built, all through an easy to reuse transformation where a bespoke Script Component was previously the only alternative. Some simple properties are available for each column selected – Behaviour The two behaviour modes offer similar functionality but with a difference. Replace, replaces tokens with the input, and Emit overwrites the whole string. Cascade Cascade allows you to define multiple expressions, each on a new line. The match expression will be processed into one operation per line, which are then processed in order at run-time. Multiple replace expressions can also be specified, again each on a new line. If there is no corresponding replace expression for a match expression line, then the last replace expression will be used instead. It is common to have multiple match expressions, but only a single replace expression. Match Expression The expression used to define the named capture groups. This is where you can analyse the data, and tag or name elements within it as found by the match expression. Replace Expression The replace determines the final output. It will reference the named groups from the match expression and assembles them into the final output. If you want to use regular expressions to validate data then try the Regular Expression Transformation. Quick Start Guide Select a column. A new output column is created for each selected column; there is no option for in-place replacement of column values. One input column can be used to populate multiple output columns, just select the column again in the lower grid, using the Input Columns drop-down selector. Amend the output column name and size as required. They default to the same as the input column selected. Amend the behaviour as required, the default is Replace. Amend the cascade option as required, the default is true. Finally enter your match and replace regular expressions Quick Sample #1 Parse an email address and extract the user and domain portions. Format as a web address passing the user portion as a URL parameter. This uses two match groups, user and host, which correspond to the text before the @ and after it respectively. Behaviour is Emit, and cascade of false, we only have a single match expression. Match Expression ^(?<user>[^@]+)@(?<host>.+)$ Replace Expression - http://www.${host}?user=${user} Results Sample Input Sample Output [email protected] http://www.adventure-works.com?user=zheng0 The component is provided as an MSI file, however to complete the installation, you will have to add the transformation to the Visual Studio toolbox manually. Right-click the toolbox, and select Choose Items.... Select the SSIS Data Flow Items tab, and then check the RegexClean Transformation from the list. Downloads The RegexClean Transformation is available for both SQL Server 2005 and SQL Server 2008. Please choose the version to match your SQL Server version, or you can install both versions and use them side by side if you have both SQL Server 2005 and SQL Server 2008 installed. RegexClean Transformation for SQL Server 2005 RegexClean Transformation for SQL Server 2008 Version History SQL Server 2005 Version 1.0.0.105 - Public Release (28 Jan 2008) SQL Server 2005 Version 1.0.0.105 - Public Release (28 Jan 2008) Screenshot

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  • TFS Build Server not finding 'Microsoft.Expression.Interactions&rsquo;

    - by Chris Skardon
    We’ve been trying to get the build server to pick up the Microsoft.Expression.Interactions.dll needed so we can use things like the ExtendedVisualStateManager and the DataStateBehavior. Adding the DataStateBehavior in Blend adds the reference to the project, so it all compiles fine on the local machine. Checking in the code into a CI server throws up some ugliness: d:\Builds\6\Source\MyFile.xaml (290): The tag 'DataStateBehavior' does not exist in XML namespace 'http://schemas.microsoft.com/expression/2010/interactions'. Errr, it should do…?? The reference is there, so… ahhhhh! A quick check of the properties and we’re using the dll from the c:\program files (x86)\ location, no wonder the build server can’t find it – let’s add the dll into our (ever expanding) ‘lib’ folder, reference that version, and check that bad boy in… No. Still No. Still get the same error. What the??? The reference is still pointing to the program files location?? Ok, so let’s modify the csproj file using the wonderful notepad, changing the reference from <Reference Include="Microsoft.Expression.Interactions, /* loadsa shizzle here */ /> to <Reference Include="Microsoft.Expression.Interactions">     <HintPath>..\Lib\Microsoft.Expression.Interactions.dll</HintPath> </Reference> Check that in, aaaand… Success!!! The reason for this (from what I can gather from here) is that we’re using the Productivity Power Tools, and they try to be clever about referencing dlls, and changed what we’d asked (i.e. for the local version) to use the original program files location.. Editing the file in notepad (sweet sweet notepad) gets around this issue… Irritating, took a while to figure this out… Meh :)

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  • PowerPoint: print slides - enlarge their size

    - by Franz
    In PowerPoint (2007), it is possible to print multiple slides on a paper as a handout. However, there is quite a lot of whitespace in between them and around them. Is there another way to enlarge the slides (I'm using the "6 per page" option)? And I don't mean "Adjust to paper size" (or whatever that's called in English), because the difference is just minimal.

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