Upload GEO Series GSE194232

[Guillermo Arroyo Ataz]

Hello,

I keep trying to upload Series GSE194232 to GEO Importer so I can get it in .gct format, but I keep getting errors. I have tried both writing the series number and uploading the soft files, but none works. Any suggestions? Thank you.

Guillermo.

[Michael Reich]

Hi Guillermo,

The problem you are experiencing occurs because the GEO series you are trying to import is RNA-seq data, and that data is not contained in the SOFT or series matrix files. In the case of GSE194232, the counts matrix is available in the GSE194232_Genes_count_table.tsv.gz file at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE194232. Unfortunately in this case, you need to unzip and manually convert this file to the GCT format, which is described at https://www.genepattern.org/file-formats-guide/#GCT. 

Please let me know if I can be of further assistance,

Michael

--
You received this message because you are subscribed to the Google Groups "GenePattern Help Forum" group.
To unsubscribe from this group and stop receiving emails from it, send an email to genepattern-he...@googlegroups.com.
To view this discussion visit https://groups.google.com/d/msgid/genepattern-help/0992bdfc-aa5c-41a3-bb82-a17d80fe12c3n%40googlegroups.com.

--

Michael Reich
Assistant Director of Bioinformatics
University of California, San Diego
9500 Gilman Dr. #0765
La Jolla, CA 92093-0765