Showing : msnbase • reset
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News: Online course: Mass Spectrometry and Proteomics with R/Bioconductor
MSnbase
8 months ago info ▴ 10
0
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0
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597
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Problem with "too large halfWindowSize" with writeMSdata after centroiding MSe data
MSnbase
21 months ago christine.wegler • 0
0
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2
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1.3k
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Error loading package MSnbase on MacOS
MSnbase
updated 2.0 years ago by 1.6k • written 2.0 years ago by • 0
0
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3
replies
1.3k
views
TMT 10 plex impurity corrections
MSnbase
updated 2.7 years ago by 1.6k • written 2.7 years ago by • 0
0
votes
7
replies
4.3k
views
LFQ shiny app from DEP package reports: Error: 'imputeMethods' is not an exported object from 'namespace:MSnbase'
MSnbase MsCoreUtils DEP
updated 2.3 years ago by ★ 1.6k • written 2.7 years ago by ▴ 40
0
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1
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1.8k
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Installation problem
MSnbase
updated 2.9 years ago by 1.6k • written 2.9 years ago by • 0
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1
reply
896
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Problem in ion intensity
MSnbase
updated 2.9 years ago by 1.6k • written 2.9 years ago by • 0
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1
reply
1.0k
views
possible problem with mzR? cannot load Msnset for proteomics analysis
MSnbase mzR Bioconductor limma
updated 3.7 years ago by 1.6k • written 3.7 years ago by • 0
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0
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792
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Which package I can use?
MSnbase DAPAR DEP
4.0 years ago yueli7 ▴ 20
1
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1
reply
1.0k
views
Missing SCANS in writeMgfData
MSnbase
updated 4.0 years ago by 1.6k • written 4.1 years ago by ▴ 40
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4
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1.7k
views
Error with xcms - requiring MSnbase 2.15.3 but not installing
software error xcms MSnbase
updated 4.3 years ago by 1.6k • written 4.3 years ago by • 0
3
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2
replies
1.0k
views
readMSData and netCDF files, only TIC intensity available
MSnbase netCDF
4.5 years ago julien.kermorvant ▴ 30
8
votes
7
replies
2.5k
views
readMSData and netCDF files, how to set polarity ?
MSnbase
updated 4.5 years ago by ★ 2.1k • written 4.5 years ago by ▴ 30
2
votes
1
reply
1.1k
views
Maximum parsimony protein assembly/inference
rforproteomics proteomics msnid msnbase
4.7 years ago daniel.magnus.bader ▴ 50
3
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4
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1.2k
views
Ion Mass to Charge Search R Function with MSnbase, Data frame as mass to charge input help
MSnbase plyr
updated 4.8 years ago by 1.6k • written 4.8 years ago by ▴ 10
0
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5
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1.5k
views
runInfo returns startTimeStamp -infinity
lcms mzR metabolomics xcms MSnbase
updated 5.2 years ago by 1.6k • written 5.2 years ago by • 0
0
votes
8
replies
3.8k
views
Getting data into (and out of) the MSnSet object
proteomics MSnbase MSnSet readMSnSet msmsTests
updated 5.3 years ago by • 0 • written 6.8 years ago by ▴ 20
4
votes
4
replies
1.4k
views
Extracting Data from MSn experiment data ("OnDiskMSnExp")
MSnbase
updated 5.3 years ago by 1.6k • written 5.3 years ago by ▴ 20
3
votes
2
replies
1.1k
views
Access list of rtime/intensity values from chromatograms object from MSnbase
MSnbase chromatograms intensity
updated 5.3 years ago by 1.6k • written 5.3 years ago by ▴ 10
0
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5
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1.4k
views
MSnbase addIdentificationData problem
software error MSnbase
updated 5.4 years ago by 1.6k • written 5.4 years ago by • 0
2
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3
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1.1k
views
MSnbase extracting individual spectrum based on precursor ion m/z
MSnbase
updated 5.5 years ago by 1.6k • written 5.5 years ago by ▴ 30
0
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4
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3.1k
views
Error when loading MSnbase package "object 'vI' not found"
msnbase xcms pheatmap
5.7 years ago lmg • 0
0
votes
6
replies
2.2k
views
Protein quantification by MSnbase package
msnbase rforproteomics
5.8 years ago • updated 5.7 years ago fgol ▴ 10
4
votes
5
replies
2.3k
views
How to convert a xlsx data file to MSnSet format?
msnbase msmstests proteomics lc-ms/ms msnID
updated 5.8 years ago by 1.6k • written 5.8 years ago by ▴ 10
0
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5
replies
2.1k
views
MSnbase package, Error in downloading data file "PXD000001" from PRIDE Repository by pxget function
MSnbase Bioconductor PRIDE rpx PXDataset
updated 2.5 years ago by 1.6k • written 5.8 years ago by ▴ 10
0
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4
replies
1.3k
views
MSnset combine error message
MSnbase
5.9 years ago kamal.fartiyal84 ▴ 10
0
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5
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4.3k
views
Errors installing RforProteomics and MSnbase packages
RforProteomics MSnbase
updated 5.9 years ago by 1.6k • written 5.9 years ago by ▴ 10
3
votes
2
replies
1.4k
views
MSnbase annotate m/z values on mass spectrum plots
msnbase
updated 5.9 years ago by 1.6k • written 6.0 years ago by ▴ 30
1
vote
2
replies
1.1k
views
quantify() method for MSnExp to MSnSet for MS1 level data only
msnbase spectrum
updated 6.2 years ago by 1.6k • written 6.2 years ago by • 0
3
votes
1
reply
1.1k
views
Does OnDiskMSnExp rewrite original data
xcms msnbase ondiskmsnexp
updated 6.3 years ago by 1.6k • written 6.3 years ago by • 0
1
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2
replies
1.7k
views
Label free quantification post FDR calculation for MS/MS Proteomics
mzid msnbase mzr
updated 6.5 years ago by 1.6k • written 6.5 years ago by ▴ 10
0
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2
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1.2k
views
How to manipulate assayData in MSnSetList
msnbase
6.6 years ago kamal.fartiyal84 ▴ 10
2
votes
4
replies
1.7k
views
calling combineFeatures twice causes duplicate row.names
msnbase duplicate rforproteomics
updated 6.8 years ago by 1.6k • written 6.8 years ago by ▴ 10
0
votes
6
replies
2.3k
views
Combining two MSnSet
msnbase
7.2 years ago • updated 6.8 years ago kamal.fartiyal84 ▴ 10
0
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1
reply
1.1k
views
Adding Identification Data to MSnbase MSn Experiment
MSnbase
7.1 years ago lau1 • 0
0
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4
replies
2.2k
views
Missing value imputation
msnbase
7.3 years ago kamal.fartiyal84 ▴ 10
0
votes
14
replies
2.8k
views
Pbase: AddIdentificationData. How can I use MSnId objects (filtered psm) to build the Proteins database
pbase MsnId mzid msnbase
updated 8.7 years ago by ▴ 80 • written 8.8 years ago by • 0
0
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2
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4.7k
views
Error: package or namespace load failed for ‘MSnbase’
MSnbase
updated 8.7 years ago by 1.6k • written 8.7 years ago by • 0
4
votes
15
replies
3.5k
views
Converting Synapter object output into a MSnbase-compatible object
synapter msnbase
9.3 years ago • updated 9.2 years ago diana.schreier • 0
1
vote
9
replies
2.7k
views
msnbase error when adding identification data
msnbase proteomics itraq
updated 9.9 years ago by 1.6k • written 9.9 years ago by • 0
40 results • Page 1 of 1
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Answer: ANOVA like approach of edgeR by Gordon Smyth 51k
You need to clarify whether interactions are present for the two factors in your study. In the two factors do not interact, then the code y…
Answer: Create Illmina bead summary data by Gordon Smyth 51k
GenomeStudio produces IDAT files that you can read using the `read.idat` function in limma. That is the recommended way to read GenomeStudi…
Comment: Help with RSEM counts: do I transpose matrix? by NB • 0
OK thank you.
Comment: Help with RSEM counts: do I transpose matrix? by James W. MacDonald 67k
You can ask here, but please read the `DESeq2` vignette first, which should answer most questions.
Comment: Help with RSEM counts: do I transpose matrix? by NB • 0
Thank you. If I have questions about QC/normalization, do I ask them here or ask a new question?
Votes
Answer: ANOVA like approach of edgeR
Answer: ANOVA like approach of edgeR
Comment: ANOVA like approach of edgeR
Answer: Detecting genomic signatures of drug resistance breast cancer in transcriptom
Comment: Issues with BSgenome.Mmusculus.UCSC.mm39 and generating motif matrix in Signac (
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