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XCMS Data Processing
r xcms metabolomi NTA Metabolomics
updated 9 months ago by 68k • written 9 months ago by • 0
1
vote
3
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1.2k
views
Tutorial regarding metabolomics with R
Bioconductor Metabolomics xcms
updated 12 months ago by 68k • written 12 months ago by • 0
0
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1
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794
views
News: Subject: Last 2 Seats Available for Metabolomics with R/Bioconductor Course (October 7-10)
Metabolomics xcms
updated 12 months ago by • 0 • written 12 months ago by ▴ 10
0
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2
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3.9k
views
Error: BiocParallel errors
xcms msdata BiocParallel
2.2 years ago • updated 2.1 years ago mavamay • 0
0
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0
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886
views
mzTab-M in XCMS
xcms mzTab-M iterativehierarchicalprocessing FBMN
2.4 years ago Abrianna • 0
0
votes
1
reply
920
views
How to get around the warning message: mzR has been built against a different Rcpp version
xcms mzR
updated 2.6 years ago by ★ 5.0k • written 2.6 years ago by • 0
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0
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712
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XCMS normalization
xcms
2.7 years ago T.RU • 0
0
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1
reply
988
views
msPurity::spectralMatching Error in getSmeta(con, pids) : No meta data for spectra available
msPurity Metabolomics Bioconductor xcms spectralMatching
updated 2.7 years ago by • 0 • written 3.0 years ago by ▴ 10
0
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0
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712
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dont find xcmsSet for peak analysis
xcms
3.0 years ago aline.lafise • 0
1
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4
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2.1k
views
xcmsRaw not reading data files in: invalid class “xcmsFileSource” object
xcms
updated 3.2 years ago by • 0 • written 5.0 years ago by ▴ 30
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0
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1.0k
views
xcms crashes R 4.2.0, also unable to install IPO or msdata
IPO msdata xcms
3.5 years ago mba • 0
5
votes
5
replies
1.6k
views
Warning in In chromPeakSpectra: Lazy evaluation queue is not empty, results in NULL object
xcms Spectra
updated 3.6 years ago by ★ 2.1k • written 3.6 years ago by ▴ 20
0
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3
replies
2.0k
views
Warning messages during intallation of XCMS
xcms Install
updated 3.6 years ago by 68k • written 3.7 years ago by • 0
0
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0
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986
views
BiocParallel errors in XCMS peak-picking
BiocParallel xcms biocparallel
3.9 years ago noerman • 0
0
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4
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19k
views
hclust(d, method = method) : NA/NaN/Inf in foreign function call (arg 10)
R pheatmap xcms
updated 3.2 years ago by 68k • written 4.2 years ago by • 0
0
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2
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1.9k
views
colMax is not exported from the xcms package
xcms
4.4 years ago Habil Zare ▴ 200
0
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0
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1.0k
views
Mass spec intensity difference
xcms
4.5 years ago Phytochem • 0
0
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0
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1.0k
views
Running > 100 samples per group - memory issues
xcms memory findchrompeaks
4.5 years ago abrsoule ▴ 30
0
votes
0
replies
1.9k
views
BiocParallel errors with xcms
BiocParallel xcms
4.6 years ago Yuki ▴ 10
1
vote
3
replies
1.5k
views
Inconsistent peak areas ('into') with Matched Filter Param
xcms
updated 4.9 years ago by ★ 2.1k • written 5.0 years ago by ▴ 10
0
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1
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2.2k
views
convert from profile to centroid.
MassSpectrometry xcms
updated 5.0 years ago by 1.6k • written 5.0 years ago by • 0
0
votes
3
replies
1.7k
views
Use xcms but mzR occurs error
software error xcms
updated 5.2 years ago by ★ 4.0k • written 5.2 years ago by • 0
0
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4
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2.1k
views
Error with xcms - requiring MSnbase 2.15.3 but not installing
software error xcms MSnbase
updated 5.2 years ago by 1.6k • written 5.2 years ago by • 0
3
votes
2
replies
1.4k
views
How to get MS spectrum from features extracted with findChromPeaks ?
xcms
updated 5.3 years ago by ★ 2.1k • written 5.3 years ago by ▴ 30
1
vote
2
replies
1.7k
views
Baseline correction for GC-MS data
XCMS metaMS
updated 5.4 years ago by ▴ 20 • written 5.4 years ago by ▴ 30
0
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3
replies
2.5k
views
Merging and Aligning LC-MS/MS Data With XCMS (multiple scan ranges/polarities)
XCMS LC-MS LC-MS/MS Alignment
updated 5.5 years ago by ★ 2.1k • written 5.5 years ago by • 0
2
votes
13
replies
3.1k
views
Found gaps in scan time of file : cut scantime-vector at NA seconds. Error: BiocParallel errors element index: 1, 2, 3, 4, 5, 6 first error: argu…
xcms adjustRtime parameters scantime error biocparallel error
6.1 years ago abrsoule ▴ 30
0
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5
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1.9k
views
runInfo returns startTimeStamp -infinity
lcms mzR metabolomics xcms MSnbase
updated 6.1 years ago by 1.6k • written 6.1 years ago by • 0
2
votes
6
replies
2.3k
views
xcms centwave roiList error
roiList xcms centwave XIC
updated 6.2 years ago by ★ 2.1k • written 6.2 years ago by ▴ 10
0
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1
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1.7k
views
XCMS - cannot allocate vector of size **Gb when global environment is empty
r xcms
6.2 years ago garfield320 ▴ 30
2
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1
reply
1.7k
views
mzR unable to open uncorrupted mzXML file
software error mzR xcms
6.6 years ago abrsoule ▴ 30
0
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4
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3.5k
views
Error when loading MSnbase package "object 'vI' not found"
msnbase xcms pheatmap
6.6 years ago lmg • 0
0
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0
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1.4k
views
Job: Postdoctoral researcher in Computational Metabolomics
metabolomics xcms Job
6.7 years ago Johannes Rainer ★ 2.1k
0
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0
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1.8k
views
Job: Postdoctoral researcher in Computational Metabolomics
xcms metabolomics population metabolism job Job
updated 6.8 years ago by • 0 • written 6.9 years ago by ★ 2.1k
0
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4
replies
2.0k
views
Intensity discrepancy between raw data and XCMS output
xcms xcmsset intensity
7.1 years ago cpataki • 0
0
votes
9
replies
4.9k
views
Error 'names' attribute must be the same length as the vector xcms
xcms xcms3 mzxml
7.2 years ago goh • 0
3
votes
1
reply
1.3k
views
Does OnDiskMSnExp rewrite original data
xcms msnbase ondiskmsnexp
updated 7.2 years ago by 1.6k • written 7.2 years ago by • 0
0
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1
reply
2.0k
views
XCMS for GC-MS
xcms GC-MS
7.2 years ago Joe • 0
0
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4
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2.7k
views
Chromatographic peak detection failed for all files
xcms
7.3 years ago yuchiu • 0
0
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1
reply
2.0k
views
Metabolite identification package
xcms massspectrometry metabolomics
updated 7.5 years ago by ★ 2.1k • written 7.5 years ago by • 0
2
votes
4
replies
1.8k
views
Using massifquant for peak detection of generic matrix data?
xcms kalman centwave yamss
7.6 years ago james.dalgleish ▴ 30
1
vote
2
replies
3.8k
views
ReadMSData problem with xcms
xcms readmsdata
updated 7.9 years ago by ★ 2.1k • written 7.9 years ago by ▴ 30
1
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5
replies
3.9k
views
'names' attribute [12] must be the same length as the vector [6]
R xcms vector
8.0 years ago bhgyu ▴ 30
5
votes
7
replies
3.1k
views
XCMS obiwarp adjustRtime issue
xcms obiwarp adjustrtime metabolomics
updated 8.0 years ago by ★ 2.1k • written 8.0 years ago by ▴ 30
2
votes
1
reply
2.6k
views
Can XCMS search Metlin using MS/MS spectra and provide a similarity score?
xcms
updated 8.3 years ago by • 0 • written 9.7 years ago by ▴ 20
0
votes
2
replies
1.6k
views
Problem with mzR and/or Rcpp?
mzr rcpp mzr rcpp XCMS
updated 8.3 years ago by 1.6k • written 8.3 years ago by • 0
0
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0
replies
1.3k
views
xcmsFragments extract product fragment
xcms xcms2
8.3 years ago riccardo.romoli • 0
1
vote
4
replies
2.4k
views
New to mass spec data analysis
data analysis xcms Tutorial
updated 12 months ago by • 0 • written 8.6 years ago by • 0
1
vote
1
reply
1.6k
views
xcms warning message
R xcms warning message
updated 8.9 years ago by ★ 2.1k • written 8.9 years ago by • 0
0
votes
1
reply
1.6k
views
error when reading .mzML with xcms::xcmsSet
software error R mzR xcms
8.9 years ago buescher • 0
78 results • Page 1 of 2
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Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Aaron already answered your question. If you have an HDF5 file, it will be read in as a `TENxMatrix` object, which isn't actually read in -…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
Very strange. We have the same package versions. I tried adding the mtx.class, type, and delayed arguments, but it's still making the coun…
Comment: DESeq2 for candidate gene analysis by piffelpaff ▴ 20
thank you so much for answering Dr. Love!
Answer: DESeq2 for candidate gene analysis by Michael Love 43k
Your plan 1 is reasonable. Run DESeq2 on the whole dataset to obtain size factors and moderated dispersion estimates and then extract the u…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Oh. ``` > z <- read10xCounts(c(tmpdir, tmpdir), mtx.class = "SVT_SparseMatrix", delayed = TRUE) > class(counts(z)) [1] "DelayedMatrix" att…
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A: Multi-level experiments in Limma
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
Answer: DESeq2 for candidate gene analysis
DESeq2 for candidate gene analysis
Answer: DESeq2 for candidate gene analysis
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