Error in proteinSummarization - possible annotation issue? about msstatstmt

[mstaniak]

Hi,
thanks for reporting the issue, can you please show us your annotation file?

[caitsimop]

Hi @mstaniak,
Would it be ok for me to email you the file?

[mstaniak]

sure, e-mail is fine

[caitsimop]

I was able to censor the annotation file to upload here in case it also can help someone else.
See below.
Thanks!
annotation_censored.txt

[mstaniak]

How many conditions are there?

[caitsimop]

We have quite a few conditions. I realized in censoring the data I inadvertently added some conditions, but in total we have 318 including the "Norm".

[mstaniak]

And how many biological replicates per condition? What is the experiment design? (Time course/group comparison)

[caitsimop]

There are 6 biological replicates (there should be 7 total IDs, one is QC and doesn't have any conditions).

It is not a time course experiment. We will be comparing treatments/groups.

[mstaniak]

Can you provide a very small subset of data to reproduce the problem? One anonymized protein that throws this error is enough. Thanks in advance, unfortunately, this annotation is not enough to locate the issue.

[caitsimop]

Hi!

Here is a small subset of censored data :

This is a protein that throws a new error:

Error in `[.data.table`(processed, , `:=`(c("PeptideSequence", "Charge"),  : 
  Supplied 2 columns to be assigned 3 items. Please see NEWS for v1.12.2.

Thanks!

[mstaniak]

Thanks. This particular error is due to underscores in peptide sequence column. There shouldn't be any

[caitsimop]

Thank you!

I ended up removing the following from the peptide sequences and I avoid the error: _ - > <

I'm now encountering the following warning:

Warning messages:
1: In survreg.fit(X, Y, weights, offset, init = init, controlvals = control,  :
  Ran out of iterations and did not converge

Is it possible to manually set more iterations for this function? Please let me know if you'd prefer I open a new issue.

[mstaniak]

Currently not, don't worry about this warning, it's not a real problem. I might add a parameter for this in a future version, but it's not important. Did the original problem disappear? Your example does throw an error for me

[caitsimop]

Thanks, @mstaniak

Yes, I no longer encountered the error once I removed any of these characters from the peptide sequences: _ - > <.