Showing : msnbase • reset
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News: Online course: Mass Spectrometry and Proteomics with R/Bioconductor
MSnbase
9 weeks ago info ▴ 10
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399
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Problem with "too large halfWindowSize" with writeMSdata after centroiding MSe data
MSnbase
15 months ago christine.wegler • 0
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2
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1.0k
views
Error loading package MSnbase on MacOS
MSnbase
updated 17 months ago by 1.6k • written 17 months ago by • 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 2.1 years ago by • 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
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Installation problem
MSnbase
updated 2.4 years ago by 1.6k • written 2.4 years ago by • 0
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1
reply
730
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Problem in ion intensity
MSnbase
updated 2.4 years ago by 1.6k • written 2.4 years ago by • 0
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1
reply
855
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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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656
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Which package I can use?
MSnbase DAPAR DEP
3.5 years ago yueli7 ▴ 20
1
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1
reply
841
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Missing SCANS in writeMgfData
MSnbase
updated 3.5 years ago by 1.6k • written 3.5 years ago by ▴ 40
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4
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1.5k
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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
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771
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readMSData and netCDF files, only TIC intensity available
MSnbase netCDF
3.9 years ago julien.kermorvant ▴ 30
8
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7
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2.1k
views
readMSData and netCDF files, how to set polarity ?
MSnbase
updated 3.9 years ago by ★ 2.0k • written 3.9 years ago by ▴ 30
2
votes
1
reply
958
views
Maximum parsimony protein assembly/inference
rforproteomics proteomics msnid msnbase
4.1 years ago daniel.magnus.bader ▴ 40
3
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4
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927
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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
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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
4
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4
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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
votes
2
replies
907
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
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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
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3
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878
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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
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4
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2.8k
views
Error when loading MSnbase package "object 'vI' not found"
msnbase xcms pheatmap
5.1 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
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5
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2.0k
views
How to convert a xlsx data file to MSnSet format?
msnbase msmstests proteomics lc-ms/ms msnID
updated 5.2 years ago by 1.6k • written 5.2 years ago by ▴ 10
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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 24 months ago by 1.6k • written 5.3 years ago by ▴ 10
0
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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
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4
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1.1k
views
MSnset combine error message
MSnbase
5.3 years ago kamal.fartiyal84 ▴ 10
3
votes
2
replies
1.1k
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
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2
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952
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
votes
1
reply
956
views
Does OnDiskMSnExp rewrite original data
xcms msnbase ondiskmsnexp
updated 5.7 years ago by 1.6k • written 5.7 years ago by • 0
1
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2
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1.4k
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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
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2
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1.1k
views
How to manipulate assayData in MSnSetList
msnbase
6.1 years ago kamal.fartiyal84 ▴ 10
2
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4
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1.4k
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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8
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3.3k
views
Getting data into (and out of) the MSnSet object
proteomics MSnbase MSnSet readMSnSet msmsTests
updated 4.7 years ago by • 0 • written 6.3 years ago by ▴ 20
0
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1
reply
925
views
Adding Identification Data to MSnbase MSn Experiment
MSnbase
6.6 years ago lau1 • 0
0
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6
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2.0k
views
Combining two MSnSet
msnbase
6.6 years ago • updated 6.3 years ago kamal.fartiyal84 ▴ 10
0
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4
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2.0k
views
Missing value imputation
msnbase
6.8 years ago kamal.fartiyal84 ▴ 10
0
votes
2
replies
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
0
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14
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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 8.2 years ago by • 0
4
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15
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3.1k
views
Converting Synapter object output into a MSnbase-compatible object
synapter msnbase
8.7 years ago • updated 8.6 years ago diana.schreier • 0
1
vote
9
replies
2.5k
views
msnbase error when adding identification data
msnbase proteomics itraq
updated 9.3 years ago by 1.6k • written 9.3 years ago by • 0
40 results • Page 1 of 1
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Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
> Any suggestions for methylation data segmentation? I think the same segmentation can be used.
Comment: deseq2 results by swbarnes2 ★ 1.3k
Cross-posted https://www.biostars.org/p/9594331/#9594458
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by Mike Smith ★ 6.5k
The other answers here are all good and demonstrate the issue with floating point comparisons nicely. I'd like to add that your particular…
Comment: More regions in union when increasing DBA$config$mergeOverlap by Ian D. ▴ 70
Nudging my question. I could do with confirmation before proceeding with my current projects. Thank you.
Comment: Extremely small p-values using Limma for proteomic data by Robert Castelo ★ 3.3k
From the point of view of visualization, I find handy the fact that raw p-values give more resolution than adjusted ones, which allows one …
Votes
A: Volcanoplot with limma - RAW P-values or Adj.P-Values
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: minfi latest update for EPIC V2 chip
A: Error in DESeqDataSet : some values in assay are not integers
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