Pseudocount TPM Normalization Gene Expression

Q&A
1

Dear all,
I have doubt about the normalization applied for RNAseq gene expression data. In the download portal says for gene expression: " Log2 transformed, using a pseudo-count of 1 " (CCLE)

On the other hand, looking on the database of “Genomics of Drug Sensitivity in Cancer” (GDSC) using the web engine tool “Orcestra” (ORCESTRA) they say that

Gene TPM Values: After estimation by the tool detailed above, gene TPM values are transformed by log2(x + 0.001).

Therefore, we can conclude that the only difference its just that you guys for the RNAseq expression data you just add 1 instead of 0.001 like the guys GDSC?

Thanks!

2

Hi, that is correct. The only difference as you mentioned is in the pseudocount value being 1 in our data reports. This does not have any significant analysis value and was mainly chosen for historical reasons and to reduce the dynamic range of expression while avoiding negative and/or infinite values. -thanks

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