data transformation of raw gene count table

[rocpengliu]

Hello
I have a gene count table from RNAseq data, should I do any data transformation such as log10, for the gene count table before submitting to pybmds for the bmd analysis?

Thank you.

[adavis10]

what format is the RNAseq data in? If you provide an example dataset I could help determine if any transformations are necessary.

[rocpengliu]

Hello

zebrafish_gene_count_groundtruth.txt

I am working a zebrafish RNAseq data for bmd analysis, attached are the gene count table from kallisto.
The first column are the gene id, and the other columns are 10 does treatments with 3 biological repeats for each dose.

If this is for the differentially expressed gene identification, some normalizations such as log2, or upper quantile, or relative log expression transformation is usually applied before processing with edgeR or limma.

So, I am wondering if the bmds needs the normalization as identification of differentially expressed genes seems not required for bmds.

Very appreciated your response.