Error dataProcess

MSstats

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Error dataProcess <1957>  2014-01-29
 
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.
 
 
<2166> responded:  2014-02-10
Hi,

I have the same problem.

Thank you for your help.

Luc.
 
Meena responded:  2014-02-19
Hi All,

Thank you for using MSstats and suggestions. The newest version(v2.1.5) is updated which improve some options and this error message. If you want to get announcement of new version release, please sign up MSstats Google group (https://groups.google.com/forum/#!forum/msstats)

1. normalization options : new version of MSstats external tool in skyline has normalization options. Please check the tutorial (MSstats Group Study statistics_2.1.5.pdf). We will keep updating options in MSstats external tool.

2. Error message : MSstats requires that the input data structure contains a separate row for each missing intensity of the spectral features, while denoting the missing intensities as “NA”. If the rows corresponding to the missing intensities are omitted, new version of MSstats will show the following improved error message such as :

ERROR : the input dataset has missing rows.
Missing feature intensities should be present in the dataset, and their intensities should be indicated with ‘NA’.
The missing rows are listed below.
*** Subject : ReplA, Condition : 1 has missing rows for some features
(DQTNDQVTVDSATATLK_2_y10_NA, DQTNDQVTVDSATATLK_2_y11_NA, DQTNDQVTVDSATATLK_2_y8_NA, DYEGKPPPVDLDR_3_y6_NA)

which means that all other subjects and conditions have information for those 4 features with any value, (actual intensities or even NA). However, there is no information at all about these 4 feature for Subject = ReplA, Condition=1. Therefore users need to check whether these 4 features are checked for subject=ReplA in condition=1.

I hope it will be helpful for your analysis.
Thanks,

Meena