Normalization -TMM

Q&A
1

Hi
I want to understand that if I have to do TMM normalization rather than using TPM as TPM is not considered a very good parameter to compare across different samples. Which file with Raw reads would be appropriate to carry out theTMM normalization?

2

Hi,

Iā€™d suggest using OmicsExpressionGenesExpectedCountProfile or OmicsExpressionTranscriptsExpectedCountProfile which contains expected counts estimated by RSEM instead of raw reads.

As a heads up, in the upcoming release we will update our RNAseq pipeline which will introduce changes in expression data. Please stay tuned for our communications and files descriptions for more details.

Best,
Simone

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3

Thanks Simone. This is helpful.
Please help me with another query as well ā€“ The data present in OmicsExpressionGenesExpectedCountProfile or OmicsExpressionTranscriptsExpectedCountProfile are log 2 transformed or general reads ?

4

They are not log2 transformed.

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