Clariom S Human Array

[Keytam Awad]

Hi,

I am new to GSEA and I am trying to upload my annotation file. I am getting an error message indicating that GSEA cannot identify probe set ID. Clariom S Array is a gene expression array, it uses “transcript cluster ID” not probe set ID. Is there anyway around this?

Thank you,

Keytam

[Anthony Castanza]

Hello Keytam,

 

"Probe Set ID" is just the name of the column called for by the file format specification, other ID types can be used in that field, it just needs to have the expected column header for the CHIP format.

 

We don’t officially support the Clariom Arrays due to raw data access issues with Affymetrix (we get the mapping information from our officially supported chips from Ensembl's Biomart and Affymetrix hasn't deposited the data for these arrays). But we maintain legacy versions of these chip files for use with Human and Mouse Clariom Arrays available from here: https://data.broadinstitute.org/gsea-msigdb/msigdb/annotations_legacy/

These files use Affymetrix's annotations with the gene symbols remapped for each MSigDB release, the current versions are for MSigDB 7.4.

You can download the appropriate version for your array and load it into GSEA the same way you'd load any other data file.

 

Let me know if you have any other questions,

 

-Anthony

 

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

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[Keytam Awad]

Hi Anthony,

Thank you for your reply. I am still getting the same message about the probe set ID.  I do not believe that it is my file because it looks like the chip file you sent me.  Is there anyway I can upload my file for you to see.

Thanks in advance.

Keytam

[Anthony Castanza]

Hi Keytam,

 

You can send files confidentially to gsea...@broadinstitute.org and I can take a look. If the file is too large to directly attach to an email, then you could upload it somewhere like google drive and share it with that address/myself (depending on how you set up access permissions).

To view this discussion on the web visit https://groups.google.com/d/msgid/gsea-help/3c3a7f8b-e4e5-4482-aa02-e38f2821ce47n%40googlegroups.com.