**10**wrote:

Hi,

I have a question concerning the "new" scaling method offered by `tximport`

called `dtuScaledTPM`

and how it affects DTU analysis.
So far I have used `scaledTPM`

which as I understand (correct me if Im wrong) scales the TPM values to library size by multiplying the TPM of a transcript of a sample with the column sum of the count matrix and thus brings them back onto count scale?
The `dtuScaledTPM`

additionally includes the transcript length into the library size info, (dividing count based library size by library size calculated from TPM*transcript length). And the transcript length is the median of transcript lengths of all transcripts in a gene ( where the transcript length itself is the average across all samples). Is this correct? And if so, why is this beneficial for DTU analysis. I understand that using `lengthScaledTPM`

is not advantageous but I cant wrap my head around why this method is better "just" because the transcript length value is the median instead of the mean?

Sorry if this is a rather confusing question. Im seeking to understand why this method should be used for DTU . It would be great to get a worst case toy example where `lengthScaledTPM`

would not work and also where lack of length scaling in `scaledTPM`

would not work well.

Thanks in advance

Fiona

**26k**• written 8 months ago by fiona.dick91 •

**10**