Showing : MSnbase • reset
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News: Online course: Mass Spectrometry and Proteomics with R/Bioconductor
MSnbase
19 months ago info ▴ 10
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0
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809
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Problem with "too large halfWindowSize" with writeMSdata after centroiding MSe data
MSnbase
2.7 years ago christine.wegler • 0
0
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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 3.5 years ago by 1.6k • written 3.5 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 3.6 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
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1
reply
1.1k
views
Problem in ion intensity
MSnbase
updated 3.8 years ago by 1.6k • written 3.8 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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968
views
Which package I can use?
MSnbase DAPAR DEP
4.9 years ago yueli7 ▴ 20
1
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1
reply
1.2k
views
Missing SCANS in writeMgfData
MSnbase
updated 4.9 years ago by 1.6k • written 4.9 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 5.1 years ago by 1.6k • written 5.1 years ago by • 0
3
votes
2
replies
1.3k
views
readMSData and netCDF files, only TIC intensity available
MSnbase netCDF
5.3 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
5.5 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 5.7 years ago by 1.6k • written 5.7 years ago by ▴ 10
0
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5
replies
1.9k
views
runInfo returns startTimeStamp -infinity
lcms mzR metabolomics xcms MSnbase
updated 6.1 years ago by 1.6k • written 6.1 years ago by • 0
0
votes
8
replies
4.4k
views
Getting data into (and out of) the MSnSet object
proteomics MSnbase MSnSet readMSnSet msmsTests
updated 6.1 years ago by • 0 • written 7.7 years ago by ▴ 20
4
votes
4
replies
1.8k
views
Extracting Data from MSn experiment data ("OnDiskMSnExp")
MSnbase
updated 6.2 years ago by 1.6k • written 6.2 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 6.2 years ago by 1.6k • written 6.2 years ago by ▴ 10
0
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5
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1.7k
views
MSnbase addIdentificationData problem
software error MSnbase
updated 6.3 years ago by 1.6k • written 6.3 years ago by • 0
2
votes
3
replies
1.4k
views
MSnbase extracting individual spectrum based on precursor ion m/z
MSnbase
updated 6.3 years ago by 1.6k • written 6.3 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
6.5 years ago lmg • 0
0
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6
replies
2.6k
views
Protein quantification by MSnbase package
msnbase rforproteomics
6.6 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
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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 3.4 years ago by 1.6k • written 6.7 years ago by ▴ 10
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4
replies
1.6k
views
MSnset combine error message
MSnbase
6.7 years ago kamal.fartiyal84 ▴ 10
0
votes
5
replies
4.9k
views
Errors installing RforProteomics and MSnbase packages
RforProteomics MSnbase
updated 6.7 years ago by 1.6k • written 6.7 years ago by ▴ 10
3
votes
2
replies
1.8k
views
MSnbase annotate m/z values on mass spectrum plots
msnbase
updated 6.8 years ago by 1.6k • written 6.8 years ago by ▴ 30
1
vote
2
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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 7.1 years ago by 1.6k • written 7.1 years ago by • 0
1
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2
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2.1k
views
Label free quantification post FDR calculation for MS/MS Proteomics
mzid msnbase mzr
updated 7.4 years ago by 1.6k • written 7.4 years ago by ▴ 10
0
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2
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1.4k
views
How to manipulate assayData in MSnSetList
msnbase
7.5 years ago kamal.fartiyal84 ▴ 10
2
votes
4
replies
2.0k
views
calling combineFeatures twice causes duplicate row.names
msnbase duplicate rforproteomics
updated 7.7 years ago by 1.6k • written 7.7 years ago by ▴ 10
0
votes
6
replies
2.7k
views
Combining two MSnSet
msnbase
8.0 years ago • updated 7.7 years ago kamal.fartiyal84 ▴ 10
0
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1
reply
1.3k
views
Adding Identification Data to MSnbase MSn Experiment
MSnbase
8.0 years ago lau1 • 0
0
votes
4
replies
2.7k
views
Missing value imputation
msnbase
8.2 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 9.6 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 9.6 years ago by 1.6k • written 9.6 years ago by • 0
4
votes
15
replies
4.1k
views
Converting Synapter object output into a MSnbase-compatible object
synapter msnbase
10.2 years ago • updated 10.0 years ago diana.schreier • 0
1
vote
9
replies
3.2k
views
msnbase error when adding identification data
msnbase proteomics itraq
updated 10.7 years ago by 1.6k • written 10.7 years ago by • 0
40 results • Page 1 of 1
Recent ...
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Comment: Help with defining groups by Phinney, Brett ▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness by massimo • 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package by ksankaran • 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
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