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MSnbase
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149
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News:
Online course: Mass Spectrometry and Proteomics with R/Bioconductor
MSnbase
8 weeks ago
info
▴ 10
0
votes
0
replies
394
views
Problem with "too large halfWindowSize" with writeMSdata after centroiding MSe data
MSnbase
15 months ago
christine.wegler
• 0
0
votes
2
replies
1.0k
views
Error loading package MSnbase on MacOS
MSnbase
updated 17 months ago by
Laurent Gatto
1.6k • written 17 months ago by
Vinicius
• 0
0
votes
3
replies
1.0k
views
TMT 10 plex impurity corrections
MSnbase
updated 2.1 years ago by
Laurent Gatto
1.6k • written 2.1 years ago by
Akul Mehta
• 0
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
Malcolm Cook
★ 1.6k • written 2.2 years ago by
Tobias
▴ 40
0
votes
1
reply
1.5k
views
Installation problem
MSnbase
updated 2.4 years ago by
Laurent Gatto
1.6k • written 2.4 years ago by
Qing
• 0
0
votes
1
reply
724
views
Problem in ion intensity
MSnbase
updated 2.4 years ago by
Laurent Gatto
1.6k • written 2.4 years ago by
imartins
• 0
0
votes
1
reply
850
views
possible problem with mzR? cannot load Msnset for proteomics analysis
MSnbase
mzR
Bioconductor
limma
updated 3.1 years ago by
Laurent Gatto
1.6k • written 3.1 years ago by
yaare
• 0
0
votes
0
replies
651
views
Which package I can use?
MSnbase
DAPAR
DEP
3.5 years ago
yueli7
▴ 20
1
vote
1
reply
833
views
Missing SCANS in writeMgfData
MSnbase
updated 3.5 years ago by
Laurent Gatto
1.6k • written 3.5 years ago by
Pedro Baldoni
▴ 40
0
votes
4
replies
1.4k
views
Error with xcms - requiring MSnbase 2.15.3 but not installing
software error
xcms
MSnbase
updated 3.7 years ago by
Laurent Gatto
1.6k • written 3.7 years ago by
kramerl
• 0
3
votes
2
replies
764
views
readMSData and netCDF files, only TIC intensity available
MSnbase
netCDF
3.9 years ago
julien.kermorvant
▴ 30
8
votes
7
replies
2.1k
views
readMSData and netCDF files, how to set polarity ?
MSnbase
updated 3.9 years ago by
Johannes Rainer
★ 2.0k • written 3.9 years ago by
julien.kermorvant
▴ 30
2
votes
1
reply
950
views
Maximum parsimony protein assembly/inference
rforproteomics
proteomics
msnid
msnbase
4.1 years ago
daniel.magnus.bader
▴ 40
3
votes
4
replies
921
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
Laurent Gatto
1.6k • written 4.3 years ago by
djshipman2011
▴ 10
0
votes
5
replies
1.3k
views
runInfo returns startTimeStamp -infinity
lcms
mzR
metabolomics
xcms
MSnbase
updated 4.7 years ago by
Laurent Gatto
1.6k • written 4.7 years ago by
pol.soladelossantos
• 0
0
votes
8
replies
3.2k
views
Getting data into (and out of) the MSnSet object
proteomics
MSnbase
MSnSet
readMSnSet
msmsTests
updated 4.7 years ago by
sutturka
• 0 • written 6.3 years ago by
moldach
▴ 20
4
votes
4
replies
1.2k
views
Extracting Data from MSn experiment data ("OnDiskMSnExp")
MSnbase
updated 4.8 years ago by
Laurent Gatto
1.6k • written 4.8 years ago by
jamesrgraham
▴ 20
3
votes
2
replies
900
views
Access list of rtime/intensity values from chromatograms object from MSnbase
MSnbase
chromatograms
intensity
updated 4.8 years ago by
Laurent Gatto
1.6k • written 4.8 years ago by
djshipman2011
▴ 10
0
votes
5
replies
1.2k
views
MSnbase addIdentificationData problem
software error
MSnbase
updated 4.9 years ago by
Laurent Gatto
1.6k • written 4.9 years ago by
jd690764
• 0
2
votes
3
replies
870
views
MSnbase extracting individual spectrum based on precursor ion m/z
MSnbase
updated 4.9 years ago by
Laurent Gatto
1.6k • written 4.9 years ago by
garfield320
▴ 30
0
votes
4
replies
2.8k
views
Error when loading MSnbase package "object 'vI' not found"
msnbase
xcms
pheatmap
5.1 years ago
lmg
• 0
0
votes
6
replies
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 5.2 years ago by
Laurent Gatto
1.6k • written 5.2 years ago by
fgol
▴ 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 23 months ago by
Laurent Gatto
1.6k • written 5.3 years ago by
fgol
▴ 10
0
votes
4
replies
1.1k
views
MSnset combine error message
MSnbase
5.3 years ago
kamal.fartiyal84
▴ 10
0
votes
5
replies
3.7k
views
Errors installing RforProteomics and MSnbase packages
RforProteomics
MSnbase
updated 5.3 years ago by
Laurent Gatto
1.6k • written 5.3 years ago by
fgol
▴ 10
3
votes
2
replies
1.1k
views
MSnbase annotate m/z values on mass spectrum plots
msnbase
updated 5.4 years ago by
Laurent Gatto
1.6k • written 5.4 years ago by
garfield320
▴ 30
1
vote
2
replies
947
views
quantify() method for MSnExp to MSnSet for MS1 level data only
msnbase
spectrum
updated 5.6 years ago by
Laurent Gatto
1.6k • written 5.6 years ago by
dgemoets
• 0
3
votes
1
reply
951
views
Does OnDiskMSnExp rewrite original data
xcms
msnbase
ondiskmsnexp
updated 5.7 years ago by
Laurent Gatto
1.6k • written 5.7 years ago by
goh
• 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
Laurent Gatto
1.6k • written 6.0 years ago by
jspmccain
▴ 10
0
votes
2
replies
1.1k
views
How to manipulate assayData in MSnSetList
msnbase
6.1 years ago
kamal.fartiyal84
▴ 10
2
votes
4
replies
1.4k
views
calling combineFeatures twice causes duplicate row.names
msnbase
duplicate
rforproteomics
updated 6.3 years ago by
Laurent Gatto
1.6k • written 6.3 years ago by
joris.vanhoutven
▴ 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
1
reply
920
views
Adding Identification Data to MSnbase MSn Experiment
MSnbase
6.6 years ago
lau1
• 0
0
votes
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
Sebastian Gibb
▴ 80 • written 8.2 years ago by
viswanathan.raghuram
• 0
0
votes
2
replies
4.4k
views
Error: package or namespace load failed for ‘MSnbase’
MSnbase
updated 8.2 years ago by
Laurent Gatto
1.6k • written 8.2 years ago by
Marie
• 0
4
votes
15
replies
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
2.4k
views
msnbase error when adding identification data
msnbase
proteomics
itraq
updated 9.3 years ago by
Laurent Gatto
1.6k • written 9.3 years ago by
queso012
• 0
40 results • Page
1 of 1
Recent ...
Replies
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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