Eduardo Eyras

Hi, NAs are not just when TPM = 0. If the numerator TPM is zero, but the gene is expressed (other transcripts have TPM >0), PSI = 0 is a...

Hi, with so many samples per condition, the "empirical" model will not be able to work. However, the error seems to be rather a formatting issue. EIther missing label or...

Hi, yes, suppa should be able to handle an unbalanced number of samples E. On Tue, 15 Jun 2021 at 01:41, antgomo ***@***.***> wrote: > Thanks Eduardo, > I'll check...

Hi, it is finding a case with SD=0. This might be one event that does not change at all, typically all zeroes. Perhaps you could try restricting the events that...

Hi, yes please send the data or part of it and I can test it please send the link to eduardo [dot] eyras [at] anu [dot] edu [dot] au Thanks...

Hi, I notice you are using "-nan 0" It could be that there are no events with no nan's? scipy is complaining for having sd = 0. This usually happens...

Hi Jason, maybe you have a high proportion of NA's per line? That is, more than half? E. On Mon, 29 Nov 2021 at 19:37, Jason ***@***.***> wrote: > Hi,...

Hi Jason, I see it now. Yes, the error is from scipy complaining that SD = 0. A standard division = 0 means that in one or more rows all...

Some options are not necessary for the classical method, so you could run: suppa.py diffSplice --method classical --input gencode.v23.all.events.ioe --psi normal.psi tumor.psi --tpm normal.tsv tumor.tsv --lower-bound 0.1 -th 1 -nan...

Hi, thanks for your email. Is the output fine? Is this the only time you could see those temporary files? I am wondering whether there was anything failing silently and...