Hello, I would be very greatful if someone could help me with a question about the "score" value in GenePattern's Comparative Marker Selection, and if it is...
Roy, The 'score' is the value of the t-test or signal-to-noise ratio-it's not a p-value. Generally, researchers use the FDR to select differentially expressed...
Hi, I have a problem running the NormalizeDataset module- an error is: R version 2.0.1 could not be found Is there updated version available? Or is there any...
Hello Vlad, It sounds like you you recently did a fresh install of GenePattern 3.1. (ie you did not upgrade from a previous version of GenePattern). Is that...
Hi all, I've got a fresh install of GenePattern 3.1 on a CentOS 4.4 box. When I try to run the ComparativeMarkerSelection on the AML data from the tutorial, I...
Ok, I figured it out. I had the 'R home" value in the Programming languages section set to the R executable file itself, rather than the directory from which...
Ok, another newbie question. I'm running into problems with the SVM module. First, using the SVM module in "training mode", I created a model file from some...
Rick, Your test should have ran successfully. This error suggests that there may something wrong with the format of the cls file. Can you please provide the...
Thanks for looking at this Marc. I've tried the sample all_aml dataset and that works just fine. So I assume it's me. :-) It's just not very clear what. ...
Rick, Sorry for the delay. There appears to be nothing wrong with the format of the cls file. In order to do further investigation I would need both your...
I'm trying to use R to interface programmatically with GenePattern. I've been following the programmers guide and have got as far as kicking off a job on the...
What you are seeing is a known bug. You can get the latest libraries with the fixes at: http://www.broad.mit.edu/~nazaire/R_programming_libs/ Regards, ...
Question: I have run an experiment with the Affymetrix U133A 2.0 Arrays. I used the Affymetrix software ( Expression Console) to normalize the data using the...
Nicolas, To create the res files to run in GenePattern you can run ExpressionFileCreator with the CEL files generated from Affymetrix. Regards, Marc-Danie...
Hi, I tried to follow the example (PepperExample.zip) given by PEPPeR GenePattern Quick Start Guide and was stuck by an error from LandmarkMatch under...
Hi, Is anyone out there using MySQL as a database backend for genepattern? If so it would be good to hear your experiences. I'm thinking it should be...
Stewart, it should be possible to do as you suggest but to my knowledge no one has yet tried it. Ted ... genepattern? If so it would be ... to..... ... ...
Hi, If you haven't yet read our module developer's guide at http://www.broad.mit.edu/cancer/software/genepattern/tutorial/gp_programmer.html, I recommend that...
Hi Michael ... I actually just deleted that message as not one minute after I sent that I stumbled across the information in the web client instructions ...
Jeff, Thanks for this information. We'll make sure that the new module functionality is described in the module developer's guide also. Best, Michael ... -- ...
I'm using Affymetrix Human Expression Arrays (1.0 ST Arrays) and I tried to use the ExpressionfileCreator. My problem is, that the ExpressionFileCreator does...
Thanks a lot for the help. I've now also provided the .cdf file for Human Gene ST 1.0 Array. However, I still get the same error: Error in just.rma(filenames =...
Josh one of the GenePattern developers made a correction to the comment I made. Here is his response: ExpressionFileCreator does not currently support this...
I would be happy to try the beta version of the new expression file creator. It would be great if you could inform me as soon it's ready. Franz ... custom cdf ...
When I follow the link to sign up to the new forum, I get an error page: Our apologies... The item you requested does not exist on this server or cannot be...
