I am trying to use GSEA for some RNA-Seq data. I've used it previously for microarray data and it worked fine. My guess is that using well-defined probe set IDs helped.
For my data, I tried using the provided gene symbols as well as symbols exactly matching what I have. It seems no matter what I do, I end up with "None of the gene sets passed the size thresholds" error.
Using GenePattern (which I assume should be the safest option), I get the following output:
Those warnings look questionable, but they are not exactly informative. Why would it say "Missing chip file" when the chip file is obviously present?
For my data, I tried using the provided gene symbols as well as symbols exactly matching what I have. It seems no matter what I do, I end up with "None of the gene sets passed the size thresholds" error.
Using GenePattern (which I assume should be the safest option), I get the following output:
Code:
1286 [INFO ] Begun importing: Chip from: /xchip/gpprod-upload/servers/genepattern/users/uploads/tmp/run4907393233174326312.tmp/chip.platform.file/1/same.chip 1334 [WARN ] Missing chip file: >/xchip/gpprod-upload/servers/genepattern/users/uploads/tmp/run4907393233174326312.tmp/chip.platform.file/1/same.chip< at edu.mit.broad.vdb.chip.FileInMemoryChip.initHere(?:?) 1502 [INFO ] Parsed from dotchip : 21862 1350 [WARN ] Missing chip file: >/xchip/gpprod-upload/servers/genepattern/users/uploads/tmp/run4907393233174326312.tmp/chip.platform.file/1/same.chip< at edu.mit.broad.vdb.chip.FileInMemoryChip.initHere(?:?) 1738 [INFO ] Collapsing dataset was done. Original: 21862x2 (ann: 21862,2,same.chip) collapsed: 860x2 (ann: 860,2,GENE_SYMBOL) to parse>c5.all.v4.0.symbols.gmt< got: [c5.all.v4.0.symbols.gmt] 1763 [INFO ] Begun importing: GeneSetMatrix from: c5.all.v4.0.symbols.gmt 2110 [INFO ] Got gsets: 1454 now preprocessing them ... min: 3 max: 500 Done removeGeneSetsSmallerThan: 3 for: 501 / 1454 Done removeGeneSetsSmallerThan: 3 for: 1001 / 1454 2259 [INFO ] Done preproc for smaller than: 3 2428 [INFO ] Renaming rpt dir on error to: error_. 2276 [WARN ] Could not rename for error to: error_. at edu.mit.broad.genome.reports.api.ToolReport.setErroredOut(?:?)
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