Topic: Looking for help: Dimensions of profile matrices do not match ! #400
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genefisher wants to merge 537 commits intoXChromatogramsfrom
Open
Topic: Looking for help: Dimensions of profile matrices do not match ! #400genefisher wants to merge 537 commits intoXChromatogramsfrom
genefisher wants to merge 537 commits intoXChromatogramsfrom
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Hi, I think something went wrong here, can you close |
Codecov Report
@@ Coverage Diff @@
## XChromatograms #400 +/- ##
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Coverage 49.17% 49.17%
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Files 79 79
Lines 19731 19731
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Hits 9702 9702
Misses 10029 10029 Continue to review full report at Codecov.
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- Export `Param` class. - Don't drop initial feature definitions in the `featureDefinitions<-` method allowing to add additional columns to this data frame.
- The `filterFile` method gains parameter `keepFeatures` to force keeping correspondence result even due filtering by samples (files).
…d code not new expected behavior and type should be 'double' rather than 'numeric'
- `featureChromatograms` gets parameters `n` and `value` to extract EICs from only the top n samples with highest intensities. - Add related unit tests and documentation.
- Add `normalize,Chromatogram` and `normalize,Chromatograms` to normalize intensities in a chromatogram object. - Add related documentation and unit tests.
PR to resolve issue #464 by fixing group matrix type
- Fix issue in conversion from `XCMSnExp` to `xcmsSet` ensuring that a phenodata `data.frame` will **always** be set. Thanks to Andris Jankevics for reporting.
Several updates, fixes etc
- Improve performance of splitting of objects for paralle processing. - Should improve the speed of `findChromPeaks`, `refineChromPeaks`, `chromPeakSpectra` and `reconstructChromPeakSpectra`.
- Further improve splitting an `XCMSnExp` object by file by first splitting the chrom peak data. - Use `extractROWS` instead of `[` for `DataFrame`.
- Small update to refineChromPeaks to use bplapply instead of bpmapply.
[DOC] Replace links to MassSpecWavelet::sav.gol() with links to peakDetectionCWT()
- Fix problem with `fillChromPeaks` after `MatchedFilterParam` peak detection on very sparse data (i.e. data with many empty spectra).
Fix problem in fillChromPeaks with sparse data
Change rgl.* to *3d
- Reimplement the `reconstructChromPeakSpectra` function for DIA data analysis to fix an issue with chrom peaks in overlapping isolation windows for SWATH data and to generally improve performance.
Improve performance for SWATH/DIA data analysis
Contributor
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shouldn't this be closed? |
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Hey ,
I met some problem in using XC MS, I can not fix by myself now. I am looking for help in here.
I divided my samples(650 samples) into two sub groups named mock and treatment and then put them into one folder to run XCMS.
When I run mock(325 samples) independently, the XC MS runs well and it works fine for me.
When I run treatment(325 samples) independently, the the XC MS also runs well.
However, when I run mock and treatment samples(650 samples) together, the XC MS shows error as follows:
Control0h_L1-50_BD7_01_38715 Create profile matrix with method 'bin' and step 0.1 ... OK
Create profile matrix with method 'bin' and step 0.1 ... OK
Control0h_L1-51_BE7_01_38716 Create profile matrix with method 'bin' and step 0.1 ... OK
Control0h_L1-52_BF7_01_38717 Create profile matrix with method 'bin' and step 0.1 ... OK
Control0h_L1-53_BG7_01_38718 Create profile matrix with method 'bin' and step 0.1 ... OK
Control0h_L1-54_BH7_01_38719 Create profile matrix with method 'bin' and step 0.1 ... OK
Control0h_L1-55_BA8_01_38720 Create profile matrix with method 'bin' and step 0.1 ... OK
Control0h_L1-56_BB8_01_38721 Create profile matrix with method 'bin' and step 0.1 ... OK
Control0h_L1-57_BC8_01_38722 Create profile matrix with method 'bin' and step 0.1 ... OK
Control0h_L1-58_BD8_01_38723 Create profile matrix with method 'bin' and step 0.1 ... OK
Control0h_L1-59_BE8_01_38724 Create profile matrix with method 'bin' and step 0.1 ... OK
Control0h_L1-6_BG1_01_38666 Create profile matrix with method 'bin' and step 0.1 ... OK
Found gaps: cut scantime-vector at 1399.01 seconds
Control0h_L1-60_BF8_01_38725 Create profile matrix with method 'bin' and step 0.1 ... OK
Error in .local(object, ...) :
Dimensions of profile matrices do not match !
Error in group(xset2, method = "density", mzwid = 0.01, sleep = 0.001, :
object 'xset2' not found
Many thanks for you in advance!