GenePattern Error Messages

The messages displayed by GenePattern and its modules are intended to be self explanatory. This page provides additional information for messages users have found unclear:

java.io.FileNotFoundException

The GSEA module displays this error when an input file name includes a hyphen (-) or if the file does not exist. If the file name includes a hyphen, remove it or change it to an underscore (_).

java.lang.NullPointerException

The SNPFileCreator module displays this error when it cannot read the input file. SNPFileCreator expects a zip file that contains Affymetrix CEL files in version 4 format (binary). Older Affymetrix CEL files may use the version 3 format (ASCII). To convert version 3 format files to version 4 format files, use the CEL File Conversion Tool found here: http://www.affymetrix.com/support/developer/tools/devnettools.affx.

java.lang.OutOfMemoryError

The module ran out of memory. Possible solutions include:

• If this error occurred when running an analysis module, increase the amount of memory allocated for running a module on the GenePattern server. In the Web Client, select Administration>Server Settings, select the Programming Languages page, and increase the amount of memory as described on that page. Note: Only a server administrator has access to these settings. If you are using the hosted GenePattern server, you are not a server administrator. If you downloaded GenePattern and are using a local GenePattern server, you are a server administrator.

• If this error occurred when running a visualizer module, increase the amount of memory allocated for running a visualizer on your desktop computer. In the Web Client, click My Settings, select the Visualizer Memory page, and use the Java Flags field to increase visualizer memory. For example, rather than using the default of -Xmx512M use -Xmx1024M.

• Reduce the size of the dataset. For example, use the PreprocessData module to filter gene expression data, removing platform noise and genes that have little variation. Or, if a dataset includes hundreds of samples, select a subset of samples for the analysis.

• Modify the parameters to reduce the amount of computation required. For example, you might reduce the number of iterations or permutations performed; or you might cluster samples or genes rather than both samples and genes.

An error occurred while saving the output file. Cause: qvalues.txt

The ComparativeMarkerSelection module displays this error when it cannot compute the false discovery rate (FDR) using a particular method (the q value method). If the module generates an .odf results file, the results in that file will be correct but will be missing the FDR results computed using the q value method. To avoid this error, use Release 3.1 of GenePattern and version 4 of the ComparativeMarkerSelection module.

Message concerning http://bioconductor.org/

The ExpressionFileCreator module displays an "http://bioconductor.org/" message the first time it downloads required information from the Bioconductor web site.

• If the download succeeds, the message can be ignored. The analysis results for the module are correct. A message similar to the following indicates that the download succeeded:

  "trying URL 'http://bioconductor.org/packages/2.0/data/ annotation/bin/macosx/universal/contrib/2.5/ hgu133acdf_1.16.0.tgz' Content type 'application/x-gzip' length 1742274 bytes opened URL ================================================== downloaded 1701Kb"

• If the download fails, the module requires additional memory. For instructions on how to increase the amount of memory allocated for an analysis module, see java.lang.OutOfMemoryError. A message similar to the following indicates that the download failed:

  "Loading required package: BiobaseLoading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Loading required package: affyio trying URL 'http://bioconductor.org/packages/2.0/data/ annotation/bin/windows/contrib/2.5/ hgu133plus2cdf_1.16.0.zip' Content type 'application/zip' length 4385300 bytes opened URL downloaded 4282Kb Error: cannot allocate vector of size 1.1 Gb Execution halted"

R version R2.0.1 could not be found

GenePattern 3.1 supports modules written for either R2.0.1 or R2.5; however, installing GenePattern 3.1 does not install the older version of R. To run modules written for R2.0.1 you must first install R2.0.1. For more information, see the GenePattern 3.1 Release Notes.