I did DE using edgeR and next want to compare expression between different genes (eg, A with B) using logCPM (edgeR output), so was wondering if
1- logCPM is expression average of all samples/conditions ? 2- ls logCPM a good representative of gene expression, like TPM, to compare expression of different genes (A with B) or to test their correlation with miRNA expression ?
Gene logCPM
GnneA 4.2
GnneB 5.2
GeneC 3.2
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written
by
BehMah •
2 answers
Better do not go with only logFC, consider the genes which have high normalized counts and difference compared to control, with logFC <2 or 1.5.
For any adequate within-sample comparison you need a measure that takes into account the feature length, so the short answer is no. You can use TMP unit. For more details https://haroldpimentel.wordpress.com/2014/05/08/what-the-fpkm-a-review-rna-seq-expression-units/
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