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Old 11-11-2015, 07:44 AM   #7
TRA
Junior Member
 
Location: United States-NJ

Join Date: Jul 2015
Posts: 6
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Hi all,
I am using edgeR flow to get gene lists of multifactorial experiment. I have 6 conditions with 3 samples per each. The problem is some of the gene lists I got end at FDR much less than what I entered and so I did not get the whole gene list. For example, the upregulated genes were completely missing in some lists. I tried increasing the number of genes the program gives using the
< gene_table<-topTags(lrt, n=40000)
but did not help. Then I tried very restreignent FDR as follow
< DE<-tp$table[tp$table$FDR<0.000001,]$GeneID
But again did not help. The last gene in one of my lists was with
Symbol Chr logFC logCPM LR PValue FDR
Hpx 7 -7.186931303 13.83923493 57.6010426 3.21E-014 3.23E-014

Any help would be appreciated!
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