Showing : MSnbase • reset
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News: Online course: Mass Spectrometry and Proteomics with R/Bioconductor
MSnbase
11 weeks ago info ▴ 10
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0
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414
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Problem with "too large halfWindowSize" with writeMSdata after centroiding MSe data
MSnbase
15 months ago christine.wegler • 0
0
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2
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1.0k
views
Error loading package MSnbase on MacOS
MSnbase
updated 18 months ago by 1.6k • written 18 months ago by • 0
0
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3
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1.0k
views
TMT 10 plex impurity corrections
MSnbase
updated 2.1 years ago by 1.6k • written 2.2 years ago by • 0
0
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7
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3.5k
views
LFQ shiny app from DEP package reports: Error: 'imputeMethods' is not an exported object from 'namespace:MSnbase'
MSnbase MsCoreUtils DEP
updated 21 months ago by ★ 1.6k • written 2.2 years ago by ▴ 40
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1
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1.5k
views
Installation problem
MSnbase
updated 2.4 years ago by 1.6k • written 2.4 years ago by • 0
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1
reply
741
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Problem in ion intensity
MSnbase
updated 2.4 years ago by 1.6k • written 2.4 years ago by • 0
0
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1
reply
869
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possible problem with mzR? cannot load Msnset for proteomics analysis
MSnbase mzR Bioconductor limma
updated 3.2 years ago by 1.6k • written 3.2 years ago by • 0
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0
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665
views
Which package I can use?
MSnbase DAPAR DEP
3.5 years ago yueli7 ▴ 20
1
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1
reply
852
views
Missing SCANS in writeMgfData
MSnbase
updated 3.5 years ago by 1.6k • written 3.5 years ago by ▴ 40
0
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4
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1.5k
views
Error with xcms - requiring MSnbase 2.15.3 but not installing
software error xcms MSnbase
updated 3.7 years ago by 1.6k • written 3.7 years ago by • 0
3
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2
replies
779
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readMSData and netCDF files, only TIC intensity available
MSnbase netCDF
4.0 years ago julien.kermorvant ▴ 30
8
votes
7
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2.1k
views
readMSData and netCDF files, how to set polarity ?
MSnbase
updated 4.0 years ago by ★ 2.0k • written 4.0 years ago by ▴ 30
2
votes
1
reply
969
views
Maximum parsimony protein assembly/inference
rforproteomics proteomics msnid msnbase
4.1 years ago daniel.magnus.bader ▴ 50
3
votes
4
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939
views
Ion Mass to Charge Search R Function with MSnbase, Data frame as mass to charge input help
MSnbase plyr
updated 4.3 years ago by 1.6k • written 4.3 years ago by ▴ 10
0
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5
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1.3k
views
runInfo returns startTimeStamp -infinity
lcms mzR metabolomics xcms MSnbase
updated 4.7 years ago by 1.6k • written 4.7 years ago by • 0
0
votes
8
replies
3.3k
views
Getting data into (and out of) the MSnSet object
proteomics MSnbase MSnSet readMSnSet msmsTests
updated 4.8 years ago by • 0 • written 6.3 years ago by ▴ 20
4
votes
4
replies
1.2k
views
Extracting Data from MSn experiment data ("OnDiskMSnExp")
MSnbase
updated 4.8 years ago by 1.6k • written 4.8 years ago by ▴ 20
3
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2
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916
views
Access list of rtime/intensity values from chromatograms object from MSnbase
MSnbase chromatograms intensity
updated 4.8 years ago by 1.6k • written 4.8 years ago by ▴ 10
0
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5
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1.2k
views
MSnbase addIdentificationData problem
software error MSnbase
updated 4.9 years ago by 1.6k • written 4.9 years ago by • 0
2
votes
3
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886
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MSnbase extracting individual spectrum based on precursor ion m/z
MSnbase
updated 4.9 years ago by 1.6k • written 4.9 years ago by ▴ 30
0
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4
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2.9k
views
Error when loading MSnbase package "object 'vI' not found"
msnbase xcms pheatmap
5.2 years ago lmg • 0
0
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6
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1.8k
views
Protein quantification by MSnbase package
msnbase rforproteomics
5.2 years ago fgol ▴ 10
4
votes
5
replies
2.0k
views
How to convert a xlsx data file to MSnSet format?
msnbase msmstests proteomics lc-ms/ms msnID
updated 5.3 years ago by 1.6k • written 5.3 years ago by ▴ 10
0
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5
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1.9k
views
MSnbase package, Error in downloading data file "PXD000001" from PRIDE Repository by pxget function
MSnbase Bioconductor PRIDE rpx PXDataset
updated 2.0 years ago by 1.6k • written 5.3 years ago by ▴ 10
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4
replies
1.1k
views
MSnset combine error message
MSnbase
5.3 years ago kamal.fartiyal84 ▴ 10
0
votes
5
replies
3.8k
views
Errors installing RforProteomics and MSnbase packages
RforProteomics MSnbase
updated 5.3 years ago by 1.6k • written 5.3 years ago by ▴ 10
3
votes
2
replies
1.2k
views
MSnbase annotate m/z values on mass spectrum plots
msnbase
updated 5.4 years ago by 1.6k • written 5.4 years ago by ▴ 30
1
vote
2
replies
962
views
quantify() method for MSnExp to MSnSet for MS1 level data only
msnbase spectrum
updated 5.7 years ago by 1.6k • written 5.7 years ago by • 0
3
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1
reply
965
views
Does OnDiskMSnExp rewrite original data
xcms msnbase ondiskmsnexp
updated 5.8 years ago by 1.6k • written 5.8 years ago by • 0
1
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2
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1.4k
views
Label free quantification post FDR calculation for MS/MS Proteomics
mzid msnbase mzr
updated 6.0 years ago by 1.6k • written 6.0 years ago by ▴ 10
0
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2
replies
1.1k
views
How to manipulate assayData in MSnSetList
msnbase
6.1 years ago kamal.fartiyal84 ▴ 10
2
votes
4
replies
1.5k
views
calling combineFeatures twice causes duplicate row.names
msnbase duplicate rforproteomics
updated 6.3 years ago by 1.6k • written 6.3 years ago by ▴ 10
0
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6
replies
2.0k
views
Combining two MSnSet
msnbase
6.7 years ago • updated 6.3 years ago kamal.fartiyal84 ▴ 10
0
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1
reply
934
views
Adding Identification Data to MSnbase MSn Experiment
MSnbase
6.6 years ago lau1 • 0
0
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4
replies
2.0k
views
Missing value imputation
msnbase
6.8 years ago kamal.fartiyal84 ▴ 10
0
votes
14
replies
2.5k
views
Pbase: AddIdentificationData. How can I use MSnId objects (filtered psm) to build the Proteins database
pbase MsnId mzid msnbase
updated 8.2 years ago by ▴ 80 • written 8.3 years ago by • 0
0
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2
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4.5k
views
Error: package or namespace load failed for ‘MSnbase’
MSnbase
updated 8.2 years ago by 1.6k • written 8.2 years ago by • 0
4
votes
15
replies
3.1k
views
Converting Synapter object output into a MSnbase-compatible object
synapter msnbase
8.8 years ago • updated 8.7 years ago diana.schreier • 0
1
vote
9
replies
2.5k
views
msnbase error when adding identification data
msnbase proteomics itraq
updated 9.4 years ago by 1.6k • written 9.4 years ago by • 0
40 results • Page 1 of 1
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Comment: ChAMP installation issue by shepherl 3.9k
We are still waiting for the goseq to respond to our requests but will take action next week if it is not resolved. ChAMP is currently una…
Comment: How to arrange multiple plots into one page in NOISeq? by baptiste.bidon • 0
Hello everyone, I am new on this site but not a noob in R (I guess). I am facing the same problem. For me, it depends on the NOIseq plot fu…
Comment: ChAMP installation issue by Tahirah • 0
Hello. Could you please share how you managed to install ChAMP in R 4.4.0? I also have R 4.4.0 and Bioconductor 3.19 version and ChAMP fail…
Answer: Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data by James W. MacDonald 66k
Yes, you can use `limma`.
Comment: Ensembl plants at annotationHub? by Johannes Rainer ★ 2.0k
You can get the `EnsDb` EnsDb.Taestivum.v112.sqlite (for Ensembl 112/ ensemblgenomes 59) [here](https://www.dropbox.com/sh/msic0luivbldmb7/…
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how to control age and gender effect in expression data using DESeq2
Answer: Error retrieving ensembl gene id using biomaRt...
Comment: LRT, more than two conditions and pairwise comparisons
Answer: Control group between 2 batches have different expression in RNAseq data
Answer: How to remove batch effect to combine RNAseq data from 2 different experiments?
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