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Dear people of the Röstlab,

Would it be possible to use your algorithm DIAalignR as well for global retention time alignment of DDA data. I would like to perform a global retention time alignment over 410 independent runs to correct the retention time and imrpove FDR for LFQ afterwards and thus would like to input mzml files which I correct and then afterwards output as modified mzml files with corrected retention time. If you have any other idea how to do this please let me know.

Best, Peer

I have this function in main.cpp file that calculates similarity matrix. It also has a separate implementation of C++ and R code.
NumericMatrix getChromSimMat(Rcpp::List l1, Rcpp::List l2)

Is it on the same line as we discussed?

Hi:

When I run the example of areaIntegrator:

data("XIC_QFNNTDIVLLEDFQK_3_DIAlignR", package = "DIAlignR")
XICs <- XIC_QFNNTDIVLLEDFQK_3_DIAlignR[["hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt"]][["4618"]]
l1 <- lapply(XICs, [[, 1)
l2 <- lapply(XICs, [[, 2)
areaIntegrator(l1, l2, left = 5203.7, right = 5268.5, "intensity_sum", "base_to_base", FALSE, TRUE)

l1 and l2 is empty.

And the parameter named baseSubtraction is not in use.

Best wishes

Hi,
I wanted to use DIAlignR for metabolomics (SWATH). I installed everything necessary for it from this website https://htmlpreview.github.io/?https://github.com/shubham1637/DIAlignR/master/vignettes/DIAlignR-vignette.html.
I converted the XICs and put them as *.chrom.mzML in the datapath "dataPath <- system.file("metabo", package = "DIAlignR") in the xics folder.
I renamed the scored_ms1ms2.osw file from Pyprophet to merged.osw and also put it in the osw folder.
I get this error message every time:

"The names in the RUN table of the osw files do not match the mzML file names.
Check if you have the correct file names.
Error in getRunNames(dataPath, oswMerged, params) :
Name mismatch between osw and mzML files.

For all analytes in all runs, keep them as NULL.
alignTargetedRuns(dataPath = dataPath, outFile = "test.csv", runs = NULL, oswMerged = TRUE, params = params)
The file merged.osw is searched.
40 runs are in the file merged.osw
0 .chrom.sqMass files were found.
The following files have no counterpart in the xics directory.
[1] "18625_PS-B1-25" "18625_PS-B1-53" "18625_PS-B1-65"
[4] "180712_PS-B1-3-46" "180712_PS-B1-3-48" "18625_PS-B1-63"
[7] "18625_PS-B1-52" "18625_PS-B1-24" "18625_PS-B1-66"
[10] "18625_PS-B1-56" "180712_PS-B1-3-90" "180712_PS-B1-3-83"
[13] "18625_PS-B1-58" "18625_PS-B1-69" "18625_PS-B1-94"
[16] "18625_PS-B1-49" "180712_PS-B1-3-103" "180712_PS-B1-3-20"
[19] "18625_PS-B1-43" "18625_PS-B1-91" "18625_PS-B1-27"
[22] "18625_PS-B1-7" "18625_PS-B1-73" "18625_PS-B1-31"
[25] "180712_PS-B1-3-101" "18625_PS-B1-99" "18625_PS-B1-96"
[28] "18625_PS-B1-119" "18625_PS-B1-130" "18625_PS-B1-98"
[31] "18625_PS-B1-134" "18625_PS-B1-133" "18625_PS-B1-18"
[34] "18625_PS-B1-23" "18625_PS-B1-16" "18625_PS-B1-62"
[37] "18625_PS-B1-109" "18625_PS-B1-117" "18625_PS-B1-60"
[40] "18625_PS-B1-136"
The names in the RUN table of the osw files do not match the mzML file names.
Check if the file names are correct.
Error in getRunNames(dataPath, oswMerged, params) :
Name mismatch between osw and mzML files."

Where is the error?

Many greetings

Hello，I have some data for the PRM method and I see that the DIA sample on sop needs to be run openswath, but a colleague of mine previously provided you with test data which only had PRM raw data and cirt list and you returned a great result, I now want to run the PRM data myself, is there any way to run the PRM data directly?

There is an issue with allocation of large arrays on the stack introduced in 72e3877 :

the issue is that you should not allocate large arrays on the stack, see https://stackoverflow.com/questions/32322915/why-does-this-array-allocation-cause-a-segfault and these arrays could become pretty large for long chromatograms (several hundred datapoints). We should allocate them on the heap.