Showing : MSnbase • reset
8
votes
7
replies
2.1k
views
readMSData and netCDF files, how to set polarity ?
MSnbase
updated 3.9 years ago by ★ 2.0k • written 3.9 years ago by ▴ 30
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
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 1.6k • written 5.2 years ago by ▴ 10
4
votes
4
replies
1.2k
views
Extracting Data from MSn experiment data ("OnDiskMSnExp")
MSnbase
updated 4.7 years ago by 1.6k • written 4.7 years ago by ▴ 20
3
votes
1
reply
948
views
Does OnDiskMSnExp rewrite original data
xcms msnbase ondiskmsnexp
updated 5.7 years ago by 1.6k • written 5.7 years ago by • 0
3
votes
2
replies
1.1k
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
3
votes
4
replies
911
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
3
votes
2
replies
896
views
Access list of rtime/intensity values from chromatograms object from MSnbase
MSnbase chromatograms intensity
updated 4.7 years ago by 1.6k • written 4.7 years ago by ▴ 10
3
votes
2
replies
759
views
readMSData and netCDF files, only TIC intensity available
MSnbase netCDF
3.9 years ago julien.kermorvant ▴ 30
2
votes
3
replies
862
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
2
votes
1
reply
949
views
Maximum parsimony protein assembly/inference
rforproteomics proteomics msnid msnbase
4.1 years ago daniel.magnus.bader ▴ 40
2
votes
4
replies
1.4k
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
1
vote
9
replies
2.4k
views
msnbase error when adding identification data
msnbase proteomics itraq
updated 9.3 years ago by 1.6k • written 9.3 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
1
vote
2
replies
942
views
quantify() method for MSnExp to MSnSet for MS1 level data only
msnbase spectrum
updated 5.6 years ago by 1.6k • written 5.6 years ago by • 0
1
vote
1
reply
826
views
Missing SCANS in writeMgfData
MSnbase
updated 3.5 years ago by 1.6k • written 3.5 years ago by ▴ 40
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 1.6k • written 5.3 years ago by ▴ 10
0
votes
4
replies
1.1k
views
MSnset combine error message
MSnbase
5.3 years ago kamal.fartiyal84 ▴ 10
0
votes
6
replies
1.7k
views
Protein quantification by MSnbase package
msnbase rforproteomics
5.2 years ago fgol ▴ 10
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
2
replies
1.1k
views
How to manipulate assayData in MSnSetList
msnbase
6.1 years ago kamal.fartiyal84 ▴ 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
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 • 0 • written 6.3 years ago by ▴ 20
0
votes
1
reply
914
views
Adding Identification Data to MSnbase MSn Experiment
MSnbase
6.5 years ago lau1 • 0
0
votes
5
replies
1.3k
views
runInfo returns startTimeStamp -infinity
lcms mzR metabolomics xcms MSnbase
updated 4.6 years ago by 1.6k • written 4.6 years ago by • 0
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
4
replies
1.9k
views
Missing value imputation
msnbase
6.8 years ago kamal.fartiyal84 ▴ 10
0
votes
2
replies
4.4k
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
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 ▴ 80 • written 8.2 years ago by • 0
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 1.6k • written 3.7 years ago by • 0
0
votes
3
replies
1.0k
views
TMT 10 plex impurity corrections
MSnbase
updated 2.1 years ago by 1.6k • written 2.1 years ago by • 0
0
votes
0
replies
644
views
Which package I can use?
MSnbase DAPAR DEP
3.5 years ago yueli7 ▴ 20
0
votes
1
reply
843
views
possible problem with mzR? cannot load Msnset for proteomics analysis
MSnbase mzR Bioconductor limma
updated 3.1 years ago by 1.6k • written 3.1 years ago by • 0
0
votes
0
replies
138
views
News: Online course: Mass Spectrometry and Proteomics with R/Bioconductor
MSnbase
7 weeks ago info ▴ 10
0
votes
1
reply
1.5k
views
Installation problem
MSnbase
updated 2.3 years ago by 1.6k • written 2.3 years ago by • 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 20 months ago by ★ 1.6k • written 2.1 years ago by ▴ 40
0
votes
2
replies
999
views
Error loading package MSnbase on MacOS
MSnbase
updated 17 months ago by 1.6k • written 17 months ago by • 0
0
votes
0
replies
390
views
Problem with "too large halfWindowSize" with writeMSdata after centroiding MSe data
MSnbase
14 months ago christine.wegler • 0
0
votes
1
reply
719
views
Problem in ion intensity
MSnbase
updated 2.3 years ago by 1.6k • written 2.3 years ago by • 0
0
votes
5
replies
3.7k
views
Errors installing RforProteomics and MSnbase packages
RforProteomics MSnbase
updated 5.3 years ago by 1.6k • written 5.3 years ago by ▴ 10
40 results • Page 1 of 1
Recent ...
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Answer: Dominance Index for Shotgun Metagenomics Data by Leo Lahti ▴ 30
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Votes
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
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