Log-transform expr? will it be log 10 or log2

[Karl Clauser]

Hi Sisi,

When selecting the option Log-transform expr? 

http://hlathena.tools/         predict-> How to

suggests that HLAthena will perform log10 (TPM+1)

I often have RNAseq expression in the form of log2(TPM) with 0 set to NA.

If I input this to HLAthena and set logtransform_expr to false, what would you expect to happen internally with HLAthena?

Would this work sensibly for HLAthena MSiCE as it provides relative expression?

What would you advise that I do?

Thanks,

--Karl

[Sisi Sarkizova]

Hi Karl, thanks for the question!

For accurate prediction with MSiCE, I would suggest to undo the log2 TPM transform (with exponentiation) and then pass the original TPM values to HLAthena and specify log-tranform = True. 

If the log2 values are passed in with log-transform=False, the distribution of TPM values won't correspond to the distribution of the learned data, i.e. the log2 values would be an 'overestimate' as compared to log10 and thus the MSiCE predictions would be higher than expected. The cases where the TPM=0 are handled via the +1 in the built-in log-transform option.

I hope this helps!

Sisi

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