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 Post subject: Confused by export files
PostPosted: Wed Sep 04, 2013 9:55 am 
I ran an analysis with GREAT and got some interesting results for GO Molecular Function. I wanted to save the data so that I could do some downstream analyses.

I clicked on Table Controls > Export > All ontology data as .tsv

The GREAT page listed:
GO Molecular Function has 3,401 terms covering 14,912 (84%) of all 17,744 genes, and 153,864 term - gene associations.
3,401 ontology terms (100%) were tested using an annotation count range of [1, Inf].

However the resulting .tsv file only has 508 lines?
$ wc -l ~/Downloads/greatExportAll.tsv
$ 508 greatExportAll.tsv
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 Post subject:
PostPosted: Mon Sep 09, 2013 10:21 pm 
Site Admin
Jessica,

As described in http://great.stanford.edu/help/display/GREAT/Export, GREAT only returns the top 500 ranked terms per ontology.

Thanks,
Bejerano Team
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PostPosted: Mon Sep 09, 2013 10:45 pm 
Ah whoops, sorry. I read that but it didn't "click."

I'd really like to be able to download everything -- I am interested in seeing if my p-value passes a Bonferroni correction but it is quite obvious even from the top 500 terms that a lot of the terms are identical (same genes and same regions). I was thinking that I could reduce the number of terms by eliminating "duplicate" terms based on the genes and regions the terms are annotating.
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 Post subject:
PostPosted: Mon Sep 16, 2013 9:43 am 
Any thoughts on whether it's possible for me to separately download the full set of terms and annotations for my data set (I only need the GO Molecular Function annotations for my data)?

I need the information to do a multiple testing correction, which in turn is necessary because I need it to evaluate the results of the permutations I conducted to try to account for LD (I posted a previous thread about that).
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