IFIproteomics/LFQbench

DIA-NN

Opened this issue · 3 comments

brvpuyve commented

Hi everyone,

I am trying to import a DIA-NN .tsv output file in the LFQbench R package, but I always receive an error when generating reports in the LFQbench format (Must extract column with a single valid subscript. x The subscript 'filename.var' can't be 'NA'. I have included the R script and a template DIA-NN output file. Can you tell me how to fix this issue?

RLFQbench_error.zip

Best,
Bart

mesontau commented

Hi Bart,

the filename variable is not defined. Try to add this line as a parameter to the FSWE.addSoftwareConfiguration command (you may find the command at the line 35 of your script):

filename.var = "File.Name",

I can not process the example file you provided because it is just too small.

Best regards,
Pedro J.

brvpuyve commented

Hi Pedro,

Thanks for the quick fix.

Now, I am receiving another error:
Error in dataSets[[experiment]] :
attempt to select less than one element in get1index

You can access the full DIA-NN report with following hyperlink: https://filesender.belnet.be/?s=download&token=434e0a18-d6c3-4b52-8f94-b805658eeb66

Thx,

Best,
Bart

mesontau commented

Hi Bart,

sorry for late reply.

You only need to change slightly the configuration you did set up:

FSWE.addSoftwareConfiguration(
softwareName = "DIANN",
input_format = "long",
input.extension = "*.tsv$",
nastrings = "0",
filename.var = "Run",
quantitative.var = "Precursor.Normalised",
protein.var = "Protein.Names",
sequence.mod.var = "Modified.Sequence",
charge.var = "Precursor.Charge"
)

As you can see, I have only changed the filename.var to "Run". I tested it with the file you provided and it works.

Do you want me to add the DIANN as one of the default configurations?

Best regards,
Pedro José.