MSstats errors

[mayank gupta]

Hi, 
I was doing analysis using MSstats library but facing many errors with my own data sets as well as with the example data sets (the same data set used in manual).

I am following the workflow with Proteome Discoverer output for DDA provided in the MSstats manual (section 4.5) but just after running (a) " quant <- PDtoMSstatsFormat(raw, annotation=annot) " line it shows multiple warnings.

In the next step of (b) data processing it has shown error. 

Am I missing something? 

Is there any other data set for which I can re-run the analysis to see if something is wrong with my Proteome Discoverer data sets? 

Warning and error messages are as follows-

(a) 

There were 50 or more warnings (use warnings() to see the first 50)

> warnings()
Warning messages:
1: In aggregator(Intensity, na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf
2: In aggregator(Intensity, na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf

(b) 

> cox.progenesis.proposed <- dataProcess(quant,

+                                        normalization='equalizeMedian',
+                                        summaryMethod="TMP",
+                                        cutoffCensored="minFeature",
+                                        censoredInt="NA",
+                                        MBimpute=TRUE,
+                                        maxQuantileforCensored=0.999)
Error in dataProcess(quant, normalization = "equalizeMedian", summaryMethod = "TMP",  :
  unused argument (cutoffCensored = "minFeature")
>

Thanks

Best Regards,

--

Mayank

 

[mayank gupta]

Data I am using for the run -  MSV000084181  (ftp://massive.ucsd.edu/MSV000084181/)

[Mateusz Staniak]

Hi,

these warnings are nothing to worry about, they just mean there were missing values. For the dataProcess error, please remove the cutoffCensored = "minFeature" parameter. Some parameters and function calls changed in v4 of MSstats. Please check the documentation for each function to see the current parameter set.

Kind regards,
Mateusz Staniak

[mayank gupta]

Yeah I already tried that before but that too fails after following step.

>test.MSstats <- groupComparison(contrast.matrix=comparison, data=processed.quant)

Error in MSstatsContrastMatrix.matrix(contrast.matrix, groups) : 

  Assertion on 'colnames of contrast matrix' failed: Must be equal to set {'Condition1','Condition2','Condition3','Condition4','Condition5'}, but is {}.

I am using 4.0.1 version of MSstats, I am also attaching the R script here.

[Mateusz Staniak]

Hi,

column names of your contrast matrix must be the same as condition labels. If you're interested in pairwise comparisons, you can use the default contrast matrix from MSstats.

Kind regards,
Mateusz