Error 1005 - The collapsed dataset was empty when used with chip
RK
Anthony Castanza
Hello,
Yes, that should be the correct chip file. Are you setting the “Collapse/Remap to gene symbols” parameter to “collapse”?
For count data, I’d also recommend expanding the “Advanced fields” section and setting the “Collapsing mode for probe sets =>1 gene parameter” to to “sum_of_probes” instead of the default “max_probe”.
If you’ve set the collapse/remap field to “Collapse” and you’re still seeing issues, could you please send a screenshot of your Run GSEA window, as well as an example from the first few lines of your dataset (including the header if using the GCT format).
Thanks,
-Anthony
Anthony S. Castanza, PhD
Curator, Molecular Signatures Database
Mesirov Lab, Department of Medicine
University of California, San Diego
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Anthony Castanza
Hi,
The screenshot of the responder.count file you send doesn’t match our file format guidelines. Please check your data file to confirm that it complies with either our GCT or TXT format specifications:
If you’re having difficulty formatting your files, or if you’re still having errors after validating your file formatting, you can send the data confidentially to gsea...@broadinstitute.org and I can take a closer look what might be going wrong here.
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RK
Anthony Castanza
Ensembl ID is the recommended ID type for RNA-seq data. Is the ID column given the required “NAME” header? In the screenshot you sent there was no entry in the cell where NAME is expected.
In addition to confirming that the header complies with the specification, you might also try adding the DESCRIPTION column (and filling the descriptions with “na”).
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RK
Anthony Castanza
Hello,
I’m not sure what might be going on here. Something is probably malformatted somewhere. It could be something as simple as a trailing space, or the file being written out from Excel with quote marks around the gene symbols. Instead of opening the file in Excel, could you open the exact file you’re importing into GSEA in a plain text editor (like notepad) and then sending a screenshot?
If we still can’t identify the problem from there, I don’t think I’ll be able to figure out precisely what the is problem without being able to take a closer look at the files. You can provide your data file to gsea...@broadinstitute.org so we can take a closer look and try to figure it out. We’ll keep the file completely confidential and only use it for debugging.
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Russell Keathley
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