LogFC and LogCPM

Question

[silas008]

Hi!

What is the diference between LogFC and LogCPM in edegR? I dont know exactly how to select my genes. Isn't LogFC normalized?

And just another question: in edgeR Rattus norvegicus has more than 30.000 genes but i've check and there are just 22.000 coding genes for this species. What are the repeated genes in edegR table?

Thank you very much

[Keyouer]

Hey, did you figure it out what LogCPM is? because I am wondering if you compare transcripts of two samples, still can't figure it out logCPM comes out from which sample even I have looked through all these answers...

[silas008]

Not really. I am not using the logCPM that came out in the final table exactly because of that. I calculate the CPM separately.

[badribio]

CPM is similar to FPKM (or TPM) but doesn't take into account transcript length

your second question can you show us the repeated genes? what about the values against them?

[silas008]

Sorry, i think it is non-coding genes, as Devon said... Thank you

Answer 1

[Devon Ryan]

LogCPM are the log counts per million, which can be understood as measuring expression level. LogFC is the log fold-change, which is the log difference between your groups.

edgeR is giving you the output appropriate for whatever you gave it. You gave it 30,000 genes, so it gave you 30,000 results. Presumably you have a bunch of non-coding genes in there.

[mohammedtoufiq91]

Referring to this post,

I have ran RNA-Seq analysis by single sample per condition using edgeR package. The output provided me three columns for each condition (logCPM, logFC, and p-value). I want to antilog the logCPM values (because another in-house pipeline does not support log normalized values, as it only supports normalized values). Does running this code makes sense [2^(logCPM values)]. Is there another way? Please advise. Thank you.

Answer 2

[Yuyin110]

If you use the flow path of trinity script get the LogFC and LogCPM, a step is that filtrate the gene which summary the all of the sample less than 2 ( rnaseqMatrix = rnaseqMatrix[rowSums(rnaseqMatrix)>=2,] ), so that 30.000 genes only 22.000 genes do the differential analysis.

[uli.arcos8]

Hi, Yuyin110

Could you please tell me where can I to see more about this information?

I want to know better about LogCPM and I am working with Trinity. But, I can´t to understand very good your example.

Regards.