Can logCPM in edgeR be used to compare expression of different genes within sample ?
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2.3 years ago
BehMah ▴ 40

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
R RNA-Seq • 1.8k views
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2.3 years ago
k.kathirvel93 ▴ 260

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.

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Thanks, but l meant using CPM to compare genes within sample.

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2.3 years ago

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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