LogFC and LogCPM



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



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.

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.

before adding your answer.

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