Obtaining normalized count sTPMs

[moutazhelal]

Dear Authors,

Thank you for reading my issue I am trying to obtain the TPM count from the Blueprint Encode Data set I used assay() to get the log transfomed counts and then applied exp() to get the TPM

is this the right way to do this

log_counts = assay(ref_1)
TPMs_count  = exp(log_counts)

Thank you very much, Best, Moutaz

[LTLA]

If the documentation on ?BlueprintEncode is accurate, the values were generated with edgeR, which uses log2-transformation. So your final step would be more accurately 2^log_counts (keeping in mind that the "logcounts" assay holds log-TPMs rather than actual log-counts).