Hi
I'm using edgeR to look for DE genes from an RNASeq data set.
Following the edgeR docs, i"ve got a set of genes w/ pvals <.01 and would like to generate a table for those genes w/ FC> 2. What I have below returns True/False for each gene. How would I generate for the TRUE set a table of values, ie:
"table.logConc" "table.logFC" "table.PValue" "table.FDR" "adjust.method" "comparison"
sum(de.com$table$p.value < 0.01)
#[1] 2408
top2408 <- topTags(de.com, n = 2408)
#UP-regulated genes
sum(top2408$table$logFC > 0)
#[1] 1189
sum(top2408$table$logFC > 1.5)
#[1] 701
sum(top2408$table$logFC > 2)
#[1] 343
Thanks
I'm using edgeR to look for DE genes from an RNASeq data set.
Following the edgeR docs, i"ve got a set of genes w/ pvals <.01 and would like to generate a table for those genes w/ FC> 2. What I have below returns True/False for each gene. How would I generate for the TRUE set a table of values, ie:
"table.logConc" "table.logFC" "table.PValue" "table.FDR" "adjust.method" "comparison"
sum(de.com$table$p.value < 0.01)
#[1] 2408
top2408 <- topTags(de.com, n = 2408)
#UP-regulated genes
sum(top2408$table$logFC > 0)
#[1] 1189
sum(top2408$table$logFC > 1.5)
#[1] 701
sum(top2408$table$logFC > 2)
#[1] 343
Thanks