Dear All I ran cuff-links/cuff-diff pipeline on my RNA-seq data. But I have some problem on how to interpret the up and down regulated genes from the cuff-diff results. I used CummeRbund for its visual interpretation.
Along with this I was trying to identify up and down genes from log2(fold-change) value generated from cuff-diff. Saw in many posts that to identify the up & down regulated genes the threshold of log2(fold change) can be set to +2 & -2 respectively and to set the significance values as < 0.05. But when we check that, those having a significance values < 0.05 are having a fold change of + or - infinity. What does that mean? How we can connect it with up and down regulation of genes?
I read all the previous posts regarding this. But I didn't get any exact concept from those posts. So please help me to clarify, how to find the up & down regulated genes. Can we consider those genes with + or - inf log2(fold change) as up/down regulated?
Thanks in Advance.