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msnbase
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145
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News:
Online course: Mass Spectrometry and Proteomics with R/Bioconductor
MSnbase
8 weeks ago
info
▴ 10
0
votes
0
replies
392
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 2.3 years ago by
Laurent Gatto
1.6k • written 2.3 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
849
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
650
views
Which package I can use?
MSnbase
DAPAR
DEP
3.5 years ago
yueli7
▴ 20
1
vote
1
reply
832
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
761
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
949
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
899
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
866
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
945
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
949
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
919
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 8.1 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
3.0k
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
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Comment: Get genomic coordinates of CpGs sites (chromosomes, genomic position)
by
Yveto
• 0
Thank for your response. It is Illumina 450 K. I use this code ```{r } library(IlluminaHumanMethylation450kanno.ilmn12.hg19) annotat…
Answer: More regions in union when increasing DBA$config$mergeOverlap
by
Rory Stark
★ 5.2k
I think the documentation is out of sync with the code. Positive values represent gaps between intervals and negative values represent how …
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
Michael Love
41k
But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
HAK
• 0
Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
ATpoint
★ 4.1k
Here the error probably means that you habe genes where expression scross all samples is the same. Rowscaling is value minus mean divided b…
Votes
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
Answer: Fold change calculation in Diffbind vs. DESEQ2?
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
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