error in DIANNtoMSstatsFormat 'Error: column(s) not found: [FragmentQuantCorrected]'

[b2k......@gmail.com]

Hi I am trying to convert a DIANN Run to MSStats format and I get this error.

I try to run

>>

input = fread('c:/JPST001583_H_12Sample/Test_6Samp/report6Samp.tsv')
annot = fread('c:/JPST001583_H_12Sample/Test_6Samp/Jul08_JPST_hum_6samp_annote.csv')
colnames(annot) = c('Condition', 'Run', 'BioReplicate')
input2 = DIANNtoMSstatsFormat(input, annotation = annot, MBR = T)
head(input2)

>>

And I get

>>

> input = fread('c:/JPST001583_H_12Sample/Test_6Samp/report6Samp.tsv') > annot = fread('c:/JPST001583_H_12Sample/Test_6Samp/Jul08_JPST_hum_6samp_annote.csv') > colnames(annot) = c('Condition', 'Run', 'BioReplicate') > input2 = DIANNtoMSstatsFormat(input, annotation = annot, MBR = T) INFO [2024-07-10 12:49:51] ** Raw data from DIANN imported successfully. Error: column(s) not found: [FragmentQuantCorrected] > head(input2) Error: object 'input2' not found

>>

I don't see FragmentQuantCorrected column in report.tsv file

I gave attached a shortened report and annote file

Thanks

B

[b2k......@gmail.com]

BTW it is a new DIA-NN release 1.9 on jun 7th.   I will try to post on their page as well.

[b2k......@gmail.com]

Vadim replied

Might need to take this into account for DIA-NN 1.9

>>
I opened report.tsv and I could not find column FragmentQuantCorrected. Closest column I find is Fragment.Quant.Raw.
Did new version remove FragmentQuantCorrected? Do you think I could use Fragment.Quant.Raw as FragmentQuantCorrected?

vdemichev commented 23 minutes ago
Yes, can just rename the column. The reason the corrected one was removed is because the correction algorithm was removed from DIA-NN, as it’s not needed with QuantUMS.

Best,
Vadim

Thanks for the reply and explanation. I did modify the report.tsv in Excel by duplicating Fragment.Quant.Raw and renaming one Fragment.Quant.Corrected, and then the converter ran.

>>

On Wednesday, July 10, 2024 at 12:54:00 PM UTC-7 b2k......@gmail.com wrote:

[Anthony Wu]

Hi,

There DIANNtoMSstatsFormat converter also has a new parameter called "quantificationColumn".  You can set this to "FragmentQuantRaw".  For example:

output = DIANNtoMSstatsFormat(input, annotation = annot, quantificationColumn = "FragmentQuantRaw")

Make sure to install the latest version of MSstatsConvert in bioconductor (release 3.19) to access this new functionality.

Tony