Loading chip files for Preranked GSEA v3.0

[gosge...@gmail.com]

Hi, 

I've just downloaded v3.0 on my mac and trying to run a preranked analysis. I'm new to GSEA so have been following your User Guide, which I believe is based on v2.0. 

For a preranked analysis, the user guide has 5 required fields (gene sets database, number of permutations, ranked list, chip platform(s), and collapse dataset to gene symbols). 

However, for my v3.0 software, it is missing the last 2 options, so I cannot add my chip platform or collapse the dataset to match the gene symbols. 

Therefore, when I run the analysis, it displays the error "After pruning, none of the gene sets passed size thresholds".

Can you please advise me with what to do next so I can complete my analysis? I am not sure if it is an issue with v3.0 of the software, or with my mac.

Many thanks, 

Rosie

[David Eby]

Hi Rosie,

You are correct about the User Guide being for v2.0.  Unfortunately, we can only devote minimal resources to this project while we wait for word on extended funding, so we have not been able to tackle a number of things - documentation updates among them.

We removed the Collapse Dataset option from the GSEA Preranked page because it had long been a source of confusion among users contacting us on our help mailing list.  Specifically, since Preranked allows a user to rank by whatever metric they choose, there's no way to be sure that the collapsing methods we provide are suitable or even valid for the metric at hand.  We recommend collapsing the dataset outside of the Preranked analysis during the ranking phase, using whatever method is suitable for your chosen metric & data.

Regards,

David

David Eby
Consultant
Cancer Informatics Development
Broad Institute of MIT and Harvard
415 Main St, Cambridge, MA 02142, USA
http://www.broadinstitute.org/cancer
http://www.gsea-msigdb.org
https://twitter.com/GSEA_MSigDB
https://twitter.com/GenePattern

[jeremy chien]

Hi David,

I have the same problem that Rosie had. A more pressing issue is not having the option of chip platform in preranked analysis. It appears that option is missing or moved to another menu. My ranked gene list contains Ensemble gene list, and I typically used ensemble gene chip platform for annotation. Because I cannot select this chip platform, it is giving me error.

Jeremy

[David Eby]

Hi Jeremy,

See my reply to Rosie for an explanation of why we removed this.  In short, there's no way for us to know that any of these collapse modes are valid when the data has been ranked with an arbitrary user-provided metric.  We recommend collapsing outside of GSEA.

I will discuss it with the team, however.  We've received this same comment several times since removing that feature, so maybe there's something we can change.  The project is on limited resources right now, however, so any changes would come much later in the year.

Another option would be to supply an unranked full dataset to "normal" GSEA and let it do the ranking with one of our given metrics.  More information is here.

If you absolutely must do this with Preranked, GSEA v2.2 is still available on our website and the feature is still present there.  We don't recommend that but it's an option.

Regards,

David

David Eby
Consultant
Cancer Informatics Development
Broad Institute of MIT and Harvard
415 Main St, Cambridge, MA 02142, USA
http://www.broadinstitute.org/cancer
http://www.gsea-msigdb.org
https://twitter.com/GSEA_MSigDB
https://twitter.com/GenePattern