Hi all,

I'm using EdgeR to generate DEGs. I used "table(MyFit$table$FDR<0.05, MyFit$table$logFC>1.5)" to calculate the number of DEGs, but not sure how I can output the list the genes based on the above donditions. I used "subset(MyFit, MyFit$table$FDR<0.05 | MyFit$table$logFC>1.5)", but was telling "Error: Two subscripts required". Any tips will be appreciated!

Thank you in advance!

Jay

Code should be placed in three backticks as shown below

# include your problematic code here with any corresponding output 
# please also include the results of running the following in an R session 

sessionInfo( )

In edgeR, the number of DE genes is counted using decideTests() and the table of DE genes is produced by topTags(). If you want to restrict to genes with FDR < 0.05, just set p = 0.05 in the topTags call.

We strongly advise against using logFC cutoffs to select DE genes. Your use of logFC > 1.5 is especially innappropriate because it will select only up-regulated genes and ignore those that are down-regulated.