Issue with fit4

[longchung90]

Hi there,

I've encountered an issue after I applied fit4 = spectraCounteBayes(fit3)

It reports this error: Error in model.frame.default(formula = logVAR ~ x) :
variable lengths differ (found for 'x')

I just happened to me recently

Thank you

[yafeng]

Please check if fit3$count is numeric number, and doesn’t contain any missing value. Yafeng 在 2024年8月7日，09:05，Long Chung ***@***.***> 写道：  Hi there, I've encountered an issue after I applied fit4 = spectraCounteBayes(fit3) It reports this error: Error in model.frame.default(formula = logVAR ~ x) : variable lengths differ (found for 'x') I just happened to me recently Thank you — Reply to this email directly, view it on GitHub<#18>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AAXG6NYYS7CQOS37N3366RTZQFXHDAVCNFSM6AAAAABMDL3S26VHI2DSMVQWIX3LMV43ASLTON2WKOZSGQ2TCOJUGAYDEMY>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[longchung90]

Hi Yafeng,

I've check fit3, they appear to be all numerical, some with negative sign.

I still got the issue over different data sets.

Feeling a bit stuck!

[yafeng]

Hi @longchung90
fit3$count is the peptide/PSM count used for quantification of this protein. It should be positive numbers (integers), negative number definitely make no sense here .
Type min(fit3$count) to check if it contains missing, negative or zeros value, these are not allowed.
You need to check if the correct data was assigned to the fit3$count variable.

Yafeng

[longchung90]

Hi Yafeng,

I did notice that my psm.count.table did contain NA values. Should I remove them from there before performing a fit4?

Thank you

[yafeng]

@longchung90
fit3$count variable stores the peptide/psm count values for all proteins, NA values are definitely not allowed.