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proteomics
•
reset
1
vote
12
replies
13k
views
Using limma for quantitative proteomics data
Microarray
Proteomics
limma
Microarray
Proteomics
limma
12.8 years ago
Yong Li
▴ 80
25
votes
9
replies
7.9k
views
voom for spectral counts
limma
voom
proteomics
spectral counts
massspectrometry
updated 10.2 years ago by
Gordon Smyth
52k • written 10.2 years ago by
Ben Neely
▴ 40
1
vote
3
replies
5.8k
views
EdgeR for proteomics data
Proteomics
Normalization
edgeR
Proteomics
Normalization
edgeR
updated 2.5 years ago by
Divya
• 0 • written 11.3 years ago by
Phinney, Brett
▴ 10
1
vote
1
reply
5.8k
views
Mfuzz: fill.NA - Warning messages: argument is not numeric or logical: returning NA
mfuzz
clustering
bioinformatics
proteomics
timecourse
updated 9.2 years ago by
Laurent Gatto
1.6k • written 9.2 years ago by
under-waterworld
• 0
5
votes
6
replies
5.6k
views
Differential protein/biomarker expression using limma: is that possible?
Proteomics
NPX
limma
updated 15 months ago by
briankleiboeker
• 0 • written 4.1 years ago by
r.i.s.alnuwaysir
▴ 10
1
vote
1
reply
5.2k
views
edgeR: pseudocounts, logConc and logFC
Proteomics
graph
edgeR
Proteomics
graph
edgeR
updated 15.0 years ago by
Mark Robinson
★ 1.1k • written 15.0 years ago by
Ann Hess
▴ 340
0
votes
0
replies
4.4k
views
Bioconductor 2.13 is released
BiocViews
aCGH
SNP
Transcription
Sequencing
miRNA
Microarray
Genetics
Proteomics
Coverage
11.5 years ago
Dan Tenenbaum
★ 8.2k
0
votes
8
replies
4.1k
views
Getting data into (and out of) the MSnSet object
proteomics
MSnbase
MSnSet
readMSnSet
msmsTests
updated 5.7 years ago by
sutturka
• 0 • written 7.3 years ago by
moldach
▴ 20
2
votes
1
reply
4.1k
views
Convert UniProt Entry Names into Gene Symbols
Proteomics
ProteomicsWorkflow
UniProt.ws
updated 4.2 years ago by
James W. MacDonald
68k • written 4.2 years ago by
Dario Strbenac
★ 1.6k
8
votes
0
replies
3.9k
views
Tutorial:
Statistics and Computing in Genome Science (CSAMA) Course Material
rnaseq
chipseq
visualization
metagenomics
proteomics
Tutorial
9.8 years ago
Martin Morgan
25k
1
vote
6
replies
3.8k
views
DEP package: Problems installing on macOS
software error
DEP
proteomics
updated 4.8 years ago by
Laurent Gatto
1.6k • written 4.8 years ago by
jp
• 0
0
votes
3
replies
3.8k
views
from RefSeq to GO terms / gene symbol to geneID
Proteomics
Coverage
Annotation
GO
Proteomics
Coverage
Annotation
GO
17.9 years ago • updated 17.8 years ago
Simon Lin
▴ 270
3
votes
4
replies
3.7k
views
Protein differential Expression analysis
differential expression
proteomics
updated 20 months ago by
ATpoint
★ 4.8k • written 7.3 years ago by
cardin.julie
• 0
1
vote
2
replies
3.6k
views
Limma: technical and biological replicates in proteomics data
limma
proteomics
replicates
updated 6.7 years ago by
Aaron Lun
★ 28k • written 6.7 years ago by
ivansilbern
• 0
1
vote
5
replies
3.6k
views
Using Limma for proteomics (2D DIGE) datasets
Proteomics
limma
impute
limmaGUI
Proteomics
limma
impute
limmaGUI
updated 9.8 years ago by
sm
• 0 • written 15.5 years ago by
Tom Wenseleers
▴ 60
8
votes
2
replies
3.5k
views
Statistical analysis of Spectral count data : edgeR, limma or others ?
spectral counts
proteomics
limma
edger
deseq
updated 9.8 years ago by
Gordon Smyth
52k • written 9.8 years ago by
eleonoregravier
▴ 70
0
votes
2
replies
3.3k
views
biomaRt to match UniProt protein IDs with protein names
Proteomics
UniProtKeywords
updated 2.1 years ago by
James W. MacDonald
68k • written 2.1 years ago by
a.a.houfani
• 0
0
votes
1
reply
3.2k
views
Import Bam index (Rsamtools)
Proteomics
Rsamtools
Proteomics
Rsamtools
updated 13.1 years ago by
Martin Morgan
25k • written 13.1 years ago by
Francesco Mancuso
▴ 110
0
votes
0
replies
3.2k
views
PhD student in Bioinformatics, Computational Biology at Technical University of Munich, Germany
Proteomics
Pathways
Proteomics
Pathways
13.7 years ago
Amin Moghaddasi
▴ 130
3
votes
1
reply
3.1k
views
Tutorial:
Mass Spectrometry Data Analysis with the Spectra Package
mass spectrometry
proteomics
metabolomics
Tutorial
written 4.5 years ago by
Johannes Rainer
★ 2.1k
1
vote
9
replies
2.9k
views
msnbase error when adding identification data
msnbase
proteomics
itraq
updated 10.3 years ago by
Laurent Gatto
1.6k • written 10.3 years ago by
queso012
• 0
0
votes
1
reply
2.9k
views
GenomeViz again : corrected link
Proteomics
genomes
Proteomics
genomes
updated 20.3 years ago by
A.J. Rossini
▴ 210 • written 20.3 years ago by
Rohit Ghai
▴ 80
0
votes
16
replies
2.8k
views
liimma and Across Array Normalisation
Microarray
Proteomics
Microarray
Proteomics
updated 11.2 years ago by
Gordon Smyth
52k • written 11.2 years ago by
Saket Choudhary
▴ 130
0
votes
1
reply
2.8k
views
limma/voom for protein intensity data
limma
proteomics
voom
updated 3.6 years ago by
ATpoint
★ 4.8k • written 3.6 years ago by
Endre Sebestyén
▴ 70
0
votes
3
replies
2.8k
views
How to carry out Gene Set Enrichment Analysis(GSEA) on an ordered list of Entrezgene ids?
Proteomics
hgu95av2
GSEABase
Proteomics
hgu95av2
GSEABase
16.8 years ago
anna freni sterrantino
▴ 120
4
votes
9
replies
2.7k
views
Limma is doing the right way to calculate the fold change?
limma
proteomics
updated 7.9 years ago by
Laurent Gatto
1.6k • written 7.9 years ago by
Bioinformatics
▴ 30
1
vote
2
replies
2.7k
views
Errors installing mzR package
proteomics
error
updated 6.1 years ago by
Laurent Gatto
1.6k • written 6.1 years ago by
pdaltron
• 0
2
votes
5
replies
2.7k
views
proteomics analysis
Proteomics
analysis
updated 2.8 years ago by
jeroen.gilis
▴ 90 • written 2.8 years ago by
Shakiba
• 0
3
votes
0
replies
2.6k
views
Job:
Postdoctoral Scientist, Statistical Bioinformatics and Proteomics, WEHI Australia
job
proteomics
Job
statistics
5.5 years ago • updated 5.3 years ago
Gordon Smyth
52k
2
votes
0
replies
2.6k
views
Job:
Bioconductor infrastructure for the integration of genomics, transcriptomics and proteomics data
proteomics
genomics
transcriptomics
software
Job
5.6 years ago
Laurent Gatto
1.6k
0
votes
0
replies
2.6k
views
8. CGHCall problems (Bernard North [guest]) : Bioconductor Digest, Vol 126, Issue 7
aCGH
RNASeq
ChIPSeq
Proteomics
Annotation
Normalization
GO
Network
Cancer
ChipName
probe
11.6 years ago
Sarah JugurnauthLittle
▴ 20
4
votes
5
replies
2.5k
views
How to convert a xlsx data file to MSnSet format?
msnbase
msmstests
proteomics
lc-ms/ms
msnID
updated 6.2 years ago by
Laurent Gatto
1.6k • written 6.2 years ago by
fgol
▴ 10
0
votes
0
replies
2.5k
views
what is the difference between iBAQ or LFQ?
Proteomics
DEP
limma
written 3.8 years ago by
barrypraveen
• 0
0
votes
0
replies
2.5k
views
Open PhD Position - Bioinformatics in collaboration with SAP
Proteomics
Proteomics
13.0 years ago
Amin Moghaddasi
▴ 130
0
votes
3
replies
2.5k
views
limma and Volcano Plots
Microarray
Proteomics
Cancer
PROcess
Microarray
Proteomics
Cancer
PROcess
updated 11.2 years ago by
Gordon Smyth
52k • written 11.2 years ago by
Saket Choudhary
▴ 130
0
votes
3
replies
2.5k
views
Problem with XCMS
xcms
metabolomics
lipidomics
proteomics
massspectrometry
9.3 years ago
Titan
• 0
0
votes
8
replies
2.5k
views
IPI to entrez id
Proteomics
GO
biomaRt
Proteomics
GO
biomaRt
14.1 years ago
Dick Beyer
★ 1.4k
3
votes
4
replies
2.4k
views
Enrichment Analysis for Shot-gun proteomics data using the ReactomePA package: problem with identities loss
reactomepa
reactome.db
reactome
proteomics
uniprot accessions
updated 7.5 years ago by
willem.ligtenberg
▴ 150 • written 7.5 years ago by
Miguel.Cosenza
▴ 10
0
votes
5
replies
2.4k
views
Package plgem for analysis of spectral counts, was 'limma for spectral counts'
Microarray
Proteomics
limma
plgem
Microarray
Proteomics
limma
plgem
updated 14.5 years ago by
Yolande Tra
▴ 120 • written 14.5 years ago by
Pavelka, Norman
▴ 70
1
vote
8
replies
2.4k
views
DESEQ2 and continuous data
proteomics
deseq2
9.2 years ago
carandres74
• 0
0
votes
2
replies
2.4k
views
Limma Differential Analysis on Proteomics data
Proteomics
limma
Limma
DifferentialExpression
updated 3.2 years ago by
Gordon Smyth
52k • written 3.2 years ago by
Mrinal.singh06
• 0
0
votes
0
replies
2.4k
views
Job:
Abbvie -- Senior Manager/Associate Director, Exploratory Statistics
genomics
genetics
proteomics
rnaseq
microarray
Job
10.1 years ago
Feng Hong
• 0
1
vote
1
reply
2.3k
views
Job:
junior level position in proteomics/data science
proteomics
machine learning
git
docker
Job
updated 7.3 years ago by
karimse07
• 0 • written 7.5 years ago by
petyuk
▴ 70
1
vote
0
replies
2.3k
views
News:
May Institute 2018 - Computation and statistics for mass spectrometry and proteomics at Northeastern University in Boston
bioconductor
training
course
msstats
proteomics
News
7.3 years ago
mnchoi67
▴ 40
0
votes
9
replies
2.2k
views
RforProteomics workflow troubleshooting
proteomics
8.8 years ago
yockpingchow
• 0
2
votes
5
replies
2.2k
views
NA coefficients values for samples with all zeros
limmagui
proteomics
9.4 years ago
vedran.franke
• 0
3
votes
3
replies
2.2k
views
Limma repeated-measures model: Partial NA coefficients
Proteomics
limma
repeated-measures
updated 2.3 years ago by
Gordon Smyth
52k • written 2.3 years ago by
Luís C.
• 0
2
votes
12
replies
2.2k
views
msmsTests, NA values in test.results output
Proteomics
msmstests
FDR
updated 6.5 years ago by
Laurent Gatto
1.6k • written 6.5 years ago by
laural710
• 0
6
votes
6
replies
2.2k
views
limma:arrayWeights() and the "prior.n" parameter for biological replicates? (PROTEOMICS)
Proteomics
limma
StatisticalMethod
updated 4.1 years ago by
Gordon Smyth
52k • written 4.1 years ago by
Steve
▴ 10
0
votes
0
replies
2.2k
views
Post Doc position, Berlin Germany
Sequencing
Microarray
Proteomics
Pathways
Network
Cancer
Sequencing
Microarray
Proteomics
16.0 years ago
Paul Hammer
▴ 220
50 results • Page
1 of 1
Recent ...
Replies
Comment: FlowSOM library requires igraph but igraph does not install
by
Szabolcs
• 0
The R/igraph Installation FAQ covers most issues: https://r.igraph.org/articles/installation-troubleshooting.html
Comment: edgeR::cpm() results in negative values from raw counts of 0
by
Kinnary
▴ 20
Thank you very much for the vis suggestion!
Comment: edgeR::cpm() results in negative values from raw counts of 0
by
Kinnary
▴ 20
Thank you very much - I appreciate the mathematical explanation and link to Dr. Phipson's thesis!
Comment: edgeR::cpm() results in negative values from raw counts of 0
by
Kinnary
▴ 20
Thank you very much - this is very clear!
Answer: How do I set up my DESeq analysis when I know a few vehicle control samples prov
by
Michael Love
43k
I think it will capture it automatically. E.g. if you use the method that focuses on genes lowly or not affected by the treatment, then the…
Votes
Comment: edgeR::cpm() results in negative values from raw counts of 0
Answer: edgeR::cpm() results in negative values from raw counts of 0
Answer: edgeR::cpm() results in negative values from raw counts of 0
edgeR::cpm() results in negative values from raw counts of 0
Answer: edgeR::cpm() results in negative values from raw counts of 0
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