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MSnbase
•
reset
0
votes
0
replies
176
views
Problem with "too large halfWindowSize" with writeMSdata after centroiding MSe data
MSnbase
7 months ago
christine.wegler
• 0
0
votes
2
replies
635
views
Error loading package MSnbase on MacOS
MSnbase
updated 10 months ago by
Laurent Gatto
1.6k • written 10 months ago by
Vinicius
• 0
0
votes
3
replies
749
views
TMT 10 plex impurity corrections
MSnbase
updated 18 months ago by
Laurent Gatto
1.6k • written 18 months ago by
Akul Mehta
• 0
0
votes
7
replies
2.6k
views
LFQ shiny app from DEP package reports: Error: 'imputeMethods' is not an exported object from 'namespace:MSnbase'
MSnbase
MsCoreUtils
DEP
updated 13 months ago by
Malcolm Cook
★ 1.6k • written 18 months ago by
Tobias
▴ 40
0
votes
1
reply
1.2k
views
Installation problem
MSnbase
updated 21 months ago by
Laurent Gatto
1.6k • written 21 months ago by
Qing
• 0
0
votes
1
reply
531
views
Problem in ion intensity
MSnbase
updated 21 months ago by
Laurent Gatto
1.6k • written 21 months ago by
imartins
• 0
0
votes
1
reply
632
views
possible problem with mzR? cannot load Msnset for proteomics analysis
MSnbase
mzR
Bioconductor
limma
updated 2.5 years ago by
Laurent Gatto
1.6k • written 2.5 years ago by
yaare
• 0
0
votes
0
replies
464
views
Which package I can use?
MSnbase
DAPAR
DEP
2.9 years ago
yueli7
▴ 20
1
vote
1
reply
663
views
Missing SCANS in writeMgfData
MSnbase
updated 2.9 years ago by
Laurent Gatto
1.6k • written 2.9 years ago by
Pedro Baldoni
▴ 40
0
votes
4
replies
1.1k
views
Error with xcms - requiring MSnbase 2.15.3 but not installing
software error
xcms
MSnbase
updated 3.1 years ago by
Laurent Gatto
1.6k • written 3.1 years ago by
kramerl
• 0
3
votes
2
replies
544
views
readMSData and netCDF files, only TIC intensity available
MSnbase
netCDF
3.3 years ago
julien.kermorvant
▴ 20
6
votes
7
replies
1.6k
views
readMSData and netCDF files, how to set polarity ?
MSnbase
updated 3.3 years ago by
Johannes Rainer
★ 2.0k • written 3.3 years ago by
julien.kermorvant
▴ 20
2
votes
1
reply
729
views
Maximum parsimony protein assembly/inference
rforproteomics
proteomics
msnid
msnbase
3.5 years ago
daniel.magnus.bader
▴ 40
3
votes
4
replies
687
views
Ion Mass to Charge Search R Function with MSnbase, Data frame as mass to charge input help
MSnbase
plyr
updated 3.7 years ago by
Laurent Gatto
1.6k • written 3.7 years ago by
djshipman2011
▴ 10
0
votes
5
replies
956
views
runInfo returns startTimeStamp -infinity
lcms
mzR
metabolomics
xcms
MSnbase
updated 4.1 years ago by
Laurent Gatto
1.6k • written 4.1 years ago by
pol.soladelossantos
• 0
0
votes
8
replies
2.6k
views
Getting data into (and out of) the MSnSet object
proteomics
MSnbase
MSnSet
readMSnSet
msmsTests
updated 4.1 years ago by
sutturka
• 0 • written 5.7 years ago by
moldach
▴ 20
4
votes
4
replies
891
views
Extracting Data from MSn experiment data ("OnDiskMSnExp")
MSnbase
updated 4.2 years ago by
Laurent Gatto
1.6k • written 4.2 years ago by
jamesrgraham
▴ 20
3
votes
2
replies
690
views
Access list of rtime/intensity values from chromatograms object from MSnbase
MSnbase
chromatograms
intensity
updated 4.2 years ago by
Laurent Gatto
1.6k • written 4.2 years ago by
djshipman2011
▴ 10
0
votes
5
replies
945
views
MSnbase addIdentificationData problem
software error
MSnbase
updated 4.3 years ago by
Laurent Gatto
1.6k • written 4.3 years ago by
jd690764
• 0
2
votes
3
replies
659
views
MSnbase extracting individual spectrum based on precursor ion m/z
MSnbase
updated 4.3 years ago by
Laurent Gatto
1.6k • written 4.3 years ago by
garfield320
▴ 30
0
votes
4
replies
2.5k
views
Error when loading MSnbase package "object 'vI' not found"
msnbase
xcms
pheatmap
4.5 years ago
lmg
• 0
0
votes
6
replies
1.3k
views
Protein quantification by MSnbase package
msnbase
rforproteomics
4.6 years ago
fgol
▴ 10
4
votes
5
replies
1.6k
views
How to convert a xlsx data file to MSnSet format?
msnbase
msmstests
proteomics
lc-ms/ms
msnID
updated 4.6 years ago by
Laurent Gatto
1.6k • written 4.6 years ago by
fgol
▴ 10
0
votes
5
replies
1.5k
views
MSnbase package, Error in downloading data file "PXD000001" from PRIDE Repository by pxget function
MSnbase
Bioconductor
PRIDE
rpx
PXDataset
updated 16 months ago by
Laurent Gatto
1.6k • written 4.7 years ago by
fgol
▴ 10
0
votes
4
replies
864
views
MSnset combine error message
MSnbase
4.7 years ago
kamal.fartiyal84
▴ 10
0
votes
5
replies
3.1k
views
Errors installing RforProteomics and MSnbase packages
RforProteomics
MSnbase
updated 4.7 years ago by
Laurent Gatto
1.6k • written 4.7 years ago by
fgol
▴ 10
3
votes
2
replies
886
views
MSnbase annotate m/z values on mass spectrum plots
msnbase
updated 4.8 years ago by
Laurent Gatto
1.6k • written 4.8 years ago by
garfield320
▴ 30
1
vote
2
replies
756
views
quantify() method for MSnExp to MSnSet for MS1 level data only
msnbase
spectrum
updated 5.0 years ago by
Laurent Gatto
1.6k • written 5.0 years ago by
dgemoets
• 0
3
votes
1
reply
756
views
Does OnDiskMSnExp rewrite original data
xcms
msnbase
ondiskmsnexp
updated 5.1 years ago by
Laurent Gatto
1.6k • written 5.1 years ago by
goh
• 0
1
vote
2
replies
1.1k
views
Label free quantification post FDR calculation for MS/MS Proteomics
mzid
msnbase
mzr
updated 5.4 years ago by
Laurent Gatto
1.6k • written 5.4 years ago by
jspmccain
▴ 10
0
votes
2
replies
882
views
How to manipulate assayData in MSnSetList
msnbase
5.5 years ago
kamal.fartiyal84
▴ 10
2
votes
4
replies
1.1k
views
calling combineFeatures twice causes duplicate row.names
msnbase
duplicate
rforproteomics
updated 5.7 years ago by
Laurent Gatto
1.6k • written 5.7 years ago by
joris.vanhoutven
▴ 10
0
votes
6
replies
1.6k
views
Combining two MSnSet
msnbase
6.0 years ago • updated 5.7 years ago
kamal.fartiyal84
▴ 10
0
votes
1
reply
735
views
Adding Identification Data to MSnbase MSn Experiment
MSnbase
6.0 years ago
lau1
• 0
0
votes
4
replies
1.7k
views
Missing value imputation
msnbase
6.2 years ago
kamal.fartiyal84
▴ 10
0
votes
14
replies
2.1k
views
Pbase: AddIdentificationData. How can I use MSnId objects (filtered psm) to build the Proteins database
pbase
MsnId
mzid
msnbase
updated 7.5 years ago by
Sebastian Gibb
▴ 80 • written 7.6 years ago by
viswanathan.raghuram
• 0
0
votes
2
replies
4.2k
views
Error: package or namespace load failed for ‘MSnbase’
MSnbase
updated 7.6 years ago by
Laurent Gatto
1.6k • written 7.6 years ago by
Marie
• 0
4
votes
15
replies
2.5k
views
Converting Synapter object output into a MSnbase-compatible object
synapter
msnbase
8.1 years ago • updated 8.0 years ago
diana.schreier
• 0
1
vote
9
replies
2.1k
views
msnbase error when adding identification data
msnbase
proteomics
itraq
updated 8.7 years ago by
Laurent Gatto
1.6k • written 8.7 years ago by
queso012
• 0
39 results • Page
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Comment: DMRcate design
by
James W. MacDonald
63k
That's what identical context means.
Comment: DMRcate design
by
Jitendra
▴ 10
Thanks James, but I did not understand it clearly. Could I used same Limma design matrix for DMRcate?
Comment: Steps needed to change design (relevel factors) in DESeq2
by
jd774
• 0
Thanks for the example code, would the `"condition_1_vs_2"` and `"condition_2_vs_1"` giving same or different results on DEGs and normalize…
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Comment: filtering out lowly expressed genes by groups
by
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63k
You might want to filter first though. ``` fun <- function(deseqobj, contvec, cutoff) { lildds <- dds[rowMeans(assays(deseqobj…
Votes
Bioconductor 3.18 db0s, OrgDbs, and TxDbs now available
Comment: Timely differentially expressed genes
Comment: NPARC package y-variable
Comment: List of Deprecated Packages for Bioc3.18
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