Showing : MSnbase • reset
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
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
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
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
8
votes
7
replies
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
0
votes
7
replies
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
0
votes
6
replies
1.8k
views
Protein quantification by MSnbase package
msnbase rforproteomics
5.2 years ago fgol ▴ 10
0
votes
6
replies
2.0k
views
Combining two MSnSet
msnbase
6.6 years ago • updated 6.3 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
0
votes
5
replies
1.2k
views
MSnbase addIdentificationData problem
software error MSnbase
updated 4.9 years ago by 1.6k • written 4.9 years ago by • 0
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
votes
5
replies
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
0
votes
5
replies
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
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
0
votes
4
replies
2.0k
views
Missing value imputation
msnbase
6.8 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
votes
4
replies
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
votes
4
replies
938
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
votes
4
replies
2.9k
views
Error when loading MSnbase package "object 'vI' not found"
msnbase xcms pheatmap
5.2 years ago lmg • 0
0
votes
4
replies
1.1k
views
MSnset combine error message
MSnbase
5.3 years ago kamal.fartiyal84 ▴ 10
0
votes
3
replies
1.0k
views
TMT 10 plex impurity corrections
MSnbase
updated 2.1 years ago by 1.6k • written 2.2 years ago by • 0
2
votes
3
replies
886
views
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
3
votes
2
replies
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
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
1
vote
2
replies
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
3
votes
2
replies
779
views
readMSData and netCDF files, only TIC intensity available
MSnbase netCDF
4.0 years ago julien.kermorvant ▴ 30
0
votes
2
replies
1.1k
views
How to manipulate assayData in MSnSetList
msnbase
6.1 years ago kamal.fartiyal84 ▴ 10
0
votes
2
replies
1.0k
views
Error loading package MSnbase on MacOS
MSnbase
updated 18 months ago by 1.6k • written 18 months ago by • 0
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
1
vote
1
reply
852
views
Missing SCANS in writeMgfData
MSnbase
updated 3.5 years ago by 1.6k • written 3.5 years ago by ▴ 40
2
votes
1
reply
969
views
Maximum parsimony protein assembly/inference
rforproteomics proteomics msnid msnbase
4.1 years ago daniel.magnus.bader ▴ 50
0
votes
1
reply
934
views
Adding Identification Data to MSnbase MSn Experiment
MSnbase
6.6 years ago lau1 • 0
0
votes
1
reply
741
views
Problem in ion intensity
MSnbase
updated 2.4 years ago by 1.6k • written 2.4 years ago by • 0
0
votes
1
reply
869
views
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
0
votes
1
reply
1.5k
views
Installation problem
MSnbase
updated 2.4 years ago by 1.6k • written 2.4 years ago by • 0
3
votes
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
0
votes
0
replies
665
views
Which package I can use?
MSnbase DAPAR DEP
3.5 years ago yueli7 ▴ 20
0
votes
0
replies
414
views
Problem with "too large halfWindowSize" with writeMSdata after centroiding MSe data
MSnbase
15 months ago christine.wegler • 0
0
votes
0
replies
179
views
News: Online course: Mass Spectrometry and Proteomics with R/Bioconductor
MSnbase
11 weeks ago info ▴ 10
40 results • Page 1 of 1
Recent ...
Replies
Answer: Errors in chromosome annotation-biomaRt by James W. MacDonald 66k
If you are just using HGNC symbols for the lookup, and you are trying to get NCBI IDs, then I wouldn't use `biomaRt` because it's based on …
Comment: Help with ENmix readidat by James W. MacDonald 66k
Please don't add to posts from two years ago. Instead make a new post. Also, please read the help page for `readidat`. The only reason to …
Comment: LRT, more than two conditions and pairwise comparisons by James W. MacDonald 66k
In that case, probably easiest to subset to the groups being compared.
Comment: Help with ENmix readidat by minardsmitha ▴ 10
Did you figure this out? I have the same issue.
Comment: LRT, more than two conditions and pairwise comparisons by boczniak767 ▴ 720
Thank you for response, apparently I still don't know much about statistics. In fact I want to campare time-profiles [and the LRT has been …
Votes
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?
Comment: DESeq2- Mysterious interaction suppresses DEGs
Answer: DESeq2- Mysterious interaction suppresses DEGs
Answer: Subsetting RNAseq data | voomaByGroup()
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