Hello all!!

First of all thank you very much for this amazing software!!

I am currently running:

Skyline (64 bits) 3.5.0.9319
R version 3.2.4 (2016-03-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
MSstats_3.3.11

The problem is while running the QC for my DIA samples within Skyline.

I have 6 samples, 3 biological replicates and 2 different conditions:
mock1
rap1
mock2
rap2
mock3
rap3

And I have this error:
"*** Subject : 1, Condition : Mock has multiple rows (duplicate rows) for some ENDOGENOUS features ()"
"*** Subject : 1, Condition : Rap has multiple rows (duplicate rows) for some ENDOGENOUS features ()"
"*** Subject : 2, Condition : Mock has multiple rows (duplicate rows) for some ENDOGENOUS features ()"
"*** Subject : 2, Condition : Rap has multiple rows (duplicate rows) for some ENDOGENOUS features ()"
"*** Subject : 3, Condition : Mock has multiple rows (duplicate rows) for some ENDOGENOUS features ()"
"*** Subject : 3, Condition : Rap has multiple rows (duplicate rows) for some ENDOGENOUS features ()"
"ERROR : Please remove duplicate rows in the list above. "

My question is how can I know the duplicated field?? what do you mean with ENDOGENOUS features??
And, I guess I cannot remove my duplicates within skyline, can I??

Thank you very much!!!!

T

Hi MSstats team,

Here I met a weird problem for MSstats analysis.

(1) I have three samples, each with three replicates, were set in Skyline.

(2) However, the result showed only single logFC for each protein without indicating which two samples the value calculated from.

(3) the adj. p-values of all of 3,000 proteins were below the threshold.

It is so weird but I cannot figure out where the problem come from and thus need your help. Thanks a lot.

Best regards,

Wei Zhang

I keep having problems while installing MSstats in skyline.
Error message shown as in attachment. I’ve tried uninstalling previous version of R, deleting R folder as suggested on skyline tutorial. It still gives me these “package not available” messages. Any thoughts?

I have tried MSstats both from the Skyline external tool and from the R console. I think the dialogue window for QC, profile, and condition plots are not flexible enough (no choice for log transformation or normalisation method). Plus, from Skyline we cannot exploit the data as much, in R we can follow what is happening to our data and make comparison plots (volcano and heatmap). This is for my experience.
In R 3.0.1,I recently got a new error message that I do not understand as I have no zeros and no #N/A:

> quantData<-dataProcess(raw,logTrans=2, normalization=TRUE)
Missing feature intensities should be given by 'NA' in the abundance column.
Error in dataProcess(raw, logTrans = 2, normalization = TRUE) :


Also some people have been asking for clustering and PCA analyses.
Best.
Thank you.

HI
I’m using Skyline daily 2.4.9.56.16 on windows 7
I've successfully replicated the tutorial data treatment
But when I try to run MSstat on my DIA data from Skyline I get an error about missing value (see txt file)
I checked "integrate all" in order to always have a peak selected in Skyline but nothing changed.
To which missing value does it refer?
In the ppt I pasted some screenshot of the different grid results and of the MSstat input preview
Thanks a lot for your help
Diego