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PostPosted: Tue Aug 06, 2013 8:25 am 
I'm trying to do gene-based (rather than region-based) analysis with GREAT. I followed the instructions in this post (viewtopic.php?f=2&t=990) and created a foreground set that includes the TSSs of my gene-set as well as a background set that includes the TSSs of all genes in the knownCannonical table where TSS!=TES. However, whenever I use the background set I get an error about the foreground set not being a perfect subset. As far as I can tell it is using the following awk command.

awk '{if(FNR==NR){x[$0]=1}else{if(!x[$0]){print $0}}}' background.bed foreground.bed

Everything works fine when I exclude the background set, and I can use the background set as a foreground list, so I don't think there's anything wrong with that file. This is the error code I was given with one of my attempts 20130806-public-2.0.2-AuByAX. Any advice pointing me to where I'm going wrong would be much appreciated.
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PostPosted: Tue Aug 06, 2013 8:49 pm 
Site Admin
Hello,

If you are trying to do the gene based analysis with all the genes in GREAT (not the same as all genes in knownCanonical), consider running genome-wide GREAT with the foreground set and disabling the binomial significance and fold criteria and look at your results enriched using the hypergeometric test (http://bejerano.stanford.edu/help/display/GREAT/Statistics).

As noted in the statistics file, the foreground/background test doing a region-based hypergeometric test.

If you are still interested in running the foreground/background test, please submit your files again and post a new identifier.

Thanks,
Bejerano Team
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