comparison matrix issue

[mrudula mathew]

Hi MSstats Team,

                                I am trying to do MSstats analysis on Galaxy with  MaxQuant generated evidence and protein groups files along with annotation and comparison matrix files that I created. This is the comparison matrix I created. 

Name     Q23 Q74.  

Q23-Q74 1 -1 

  I keep getting the error "Error in MSstatsContrastMatrix.matrix(contrast.matrix, groups) : Assertion on 'colnames of contrast matrix' failed: Must be equal to set {'NA'}, but is {}. Calls: groupComparison ... MSstatsContrastMatrix.matrix -> <Anonymous> -> makeAssertion -> mstop Execution halted Can anyone please help me out in solving this issue?

[Anthony Wu]

Hi,

Could you also attach your annotation file?  That'll make it easier to assess the problem.

From initial glance, there are 2 criteria that need to be met that your matrix may not be satisfying:

• Column names of your matrix must be the same as your condition labels.  
• The matrix should include all condition labels (i.e. if you have 3 conditions, you'll have 3 columns in your contrast matrix).

Thanks,

Tony

[mrudula mathew]

Hi Tony,

           Thank you for your email. I have attached the annotation file. This is a pilot experiment. I have just two conditions -Q23 ( control) and Q74 (disease). with 3 replicates each. Please let me know if any other detail is required. Thank you for your time.

Regards,

Mrudula

[Anthony Wu]

Hey,

To clarify, does your contrast matrix include a period after Q74?

i.e. earlier you mentioned your matrix looks like:

Name     Q23 Q74.  

Q23-Q74 1 -1 

Would like to sanity check that your matrix doesn't have a period in it.  

If that isn't the problem, then to help us reproduce the issue, would you be able to also send over your msstats input file?

Thanks,

Tony

[Anthony Wu]

Hi,

Taking a look at your evidence file, the values in the `Raw file` column do not match with the values in the `Raw.file` column in your annotation file.

E.g. in the evidence file, we see "Q23_01.raw.thermo", but in the annotation, we see "Q23_01.raw".  Once you ensure your values match up completely, that bug you reported should not appear.

Thanks,

Tony