Showing : msnbase • reset
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News: Online course: Mass Spectrometry and Proteomics with R/Bioconductor
MSnbase
20 months ago info ▴ 10
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0
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851
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Problem with "too large halfWindowSize" with writeMSdata after centroiding MSe data
MSnbase
2.7 years ago christine.wegler • 0
0
votes
2
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1.5k
views
Error loading package MSnbase on MacOS
MSnbase
updated 2.9 years ago by 1.6k • written 2.9 years ago by • 0
0
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3
replies
1.7k
views
TMT 10 plex impurity corrections
MSnbase
updated 3.6 years ago by 1.6k • written 3.6 years ago by • 0
0
votes
7
replies
5.5k
views
LFQ shiny app from DEP package reports: Error: 'imputeMethods' is not an exported object from 'namespace:MSnbase'
MSnbase MsCoreUtils DEP
updated 3.2 years ago by ★ 1.6k • written 3.7 years ago by ▴ 40
0
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1
reply
2.2k
views
Installation problem
MSnbase
updated 3.8 years ago by 1.6k • written 3.8 years ago by • 0
0
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1
reply
1.1k
views
Problem in ion intensity
MSnbase
updated 3.9 years ago by 1.6k • written 3.9 years ago by • 0
0
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1
reply
1.3k
views
possible problem with mzR? cannot load Msnset for proteomics analysis
MSnbase mzR Bioconductor limma
updated 4.6 years ago by 1.6k • written 4.6 years ago by • 0
0
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0
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982
views
Which package I can use?
MSnbase DAPAR DEP
5.0 years ago yueli7 ▴ 20
1
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1
reply
1.2k
views
Missing SCANS in writeMgfData
MSnbase
updated 5.0 years ago by 1.6k • written 5.0 years ago by ▴ 40
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
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2
replies
1.3k
views
readMSData and netCDF files, only TIC intensity available
MSnbase netCDF
5.4 years ago julien.kermorvant ▴ 30
8
votes
7
replies
3.0k
views
readMSData and netCDF files, how to set polarity ?
MSnbase
updated 5.4 years ago by ★ 2.1k • written 5.4 years ago by ▴ 30
2
votes
1
reply
1.4k
views
Maximum parsimony protein assembly/inference
rforproteomics proteomics msnid msnbase
5.6 years ago daniel.magnus.bader ▴ 50
3
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4
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1.5k
views
Ion Mass to Charge Search R Function with MSnbase, Data frame as mass to charge input help
MSnbase plyr
updated 5.8 years ago by 1.6k • written 5.8 years ago by ▴ 10
0
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5
replies
1.9k
views
runInfo returns startTimeStamp -infinity
lcms mzR metabolomics xcms MSnbase
updated 6.2 years ago by 1.6k • written 6.2 years ago by • 0
0
votes
8
replies
4.5k
views
Getting data into (and out of) the MSnSet object
proteomics MSnbase MSnSet readMSnSet msmsTests
updated 6.2 years ago by • 0 • written 7.8 years ago by ▴ 20
4
votes
4
replies
1.8k
views
Extracting Data from MSn experiment data ("OnDiskMSnExp")
MSnbase
updated 6.3 years ago by 1.6k • written 6.3 years ago by ▴ 20
3
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2
replies
1.4k
views
Access list of rtime/intensity values from chromatograms object from MSnbase
MSnbase chromatograms intensity
updated 6.3 years ago by 1.6k • written 6.3 years ago by ▴ 10
0
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5
replies
1.7k
views
MSnbase addIdentificationData problem
software error MSnbase
updated 6.4 years ago by 1.6k • written 6.4 years ago by • 0
2
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3
replies
1.4k
views
MSnbase extracting individual spectrum based on precursor ion m/z
MSnbase
updated 6.4 years ago by 1.6k • written 6.4 years ago by ▴ 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
votes
6
replies
2.7k
views
Protein quantification by MSnbase package
msnbase rforproteomics
6.7 years ago fgol ▴ 10
4
votes
5
replies
2.7k
views
How to convert a xlsx data file to MSnSet format?
msnbase msmstests proteomics lc-ms/ms msnID
updated 6.7 years ago by 1.6k • written 6.7 years ago by ▴ 10
0
votes
5
replies
2.5k
views
MSnbase package, Error in downloading data file "PXD000001" from PRIDE Repository by pxget function
MSnbase Bioconductor PRIDE rpx PXDataset
updated 3.5 years ago by 1.6k • written 6.8 years ago by ▴ 10
0
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4
replies
1.6k
views
MSnset combine error message
MSnbase
6.8 years ago kamal.fartiyal84 ▴ 10
0
votes
5
replies
4.9k
views
Errors installing RforProteomics and MSnbase packages
RforProteomics MSnbase
updated 6.8 years ago by 1.6k • written 6.8 years ago by ▴ 10
3
votes
2
replies
1.9k
views
MSnbase annotate m/z values on mass spectrum plots
msnbase
updated 6.9 years ago by 1.6k • written 6.9 years ago by ▴ 30
1
vote
2
replies
1.4k
views
quantify() method for MSnExp to MSnSet for MS1 level data only
msnbase spectrum
updated 7.1 years ago by 1.6k • written 7.1 years ago by • 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
1
vote
2
replies
2.1k
views
Label free quantification post FDR calculation for MS/MS Proteomics
mzid msnbase mzr
updated 7.5 years ago by 1.6k • written 7.5 years ago by ▴ 10
0
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2
replies
1.4k
views
How to manipulate assayData in MSnSetList
msnbase
7.6 years ago kamal.fartiyal84 ▴ 10
2
votes
4
replies
2.0k
views
calling combineFeatures twice causes duplicate row.names
msnbase duplicate rforproteomics
updated 7.8 years ago by 1.6k • written 7.8 years ago by ▴ 10
0
votes
6
replies
2.7k
views
Combining two MSnSet
msnbase
8.1 years ago • updated 7.8 years ago kamal.fartiyal84 ▴ 10
0
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1
reply
1.3k
views
Adding Identification Data to MSnbase MSn Experiment
MSnbase
8.1 years ago lau1 • 0
0
votes
4
replies
2.7k
views
Missing value imputation
msnbase
8.3 years ago kamal.fartiyal84 ▴ 10
0
votes
14
replies
3.4k
views
Pbase: AddIdentificationData. How can I use MSnId objects (filtered psm) to build the Proteins database
pbase MsnId mzid msnbase
updated 9.6 years ago by ▴ 80 • written 9.7 years ago by • 0
0
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2
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5.0k
views
Error: package or namespace load failed for ‘MSnbase’
MSnbase
updated 9.7 years ago by 1.6k • written 9.7 years ago by • 0
4
votes
15
replies
4.2k
views
Converting Synapter object output into a MSnbase-compatible object
synapter msnbase
10.2 years ago • updated 10.1 years ago diana.schreier • 0
1
vote
9
replies
3.2k
views
msnbase error when adding identification data
msnbase proteomics itraq
updated 10.8 years ago by 1.6k • written 10.8 years ago by • 0
40 results • Page 1 of 1
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Comment: deseq2 filter the low counts by Michael Love 43k
Have you seen this part: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering
Comment: deseq2 filter the low counts by empty_mt • 0
Hi Michael, My matrix consists of 36 samples from 6 treatments (6 samples/ treatment), whether I adjust prefiltering parameters or not, in…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
That works. I didn't realize what you said about HDF5 files. We always keep those and archive the MTX files. I'm able to read in the file…
Comment: DESeq2 interactions by Michael Love 43k
GPT even v4 gives pretty good answers to DESeq2 questions that are similar to those already posted on the support site. I've also noticed …
Answer: Important: Bioconductor Release 3.22 Delayed by shepherl 4.2k
We will continue with the release on Thursday October 30th. We have shifted one day as originally planned. Thank you
Votes
Answer: DESeq2 interactions
Answer: Important: Bioconductor Release 3.22 Delayed
A: Multi-level experiments in Limma
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
Answer: DESeq2 for candidate gene analysis
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