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proteomics
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1
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12
replies
12k
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Using limma for quantitative proteomics data
Microarray
Proteomics
limma
Microarray
Proteomics
limma
11.9 years ago • updated 11.8 years ago
Yong Li
▴ 80
25
votes
9
replies
6.8k
views
voom for spectral counts
limma
voom
proteomics
spectral counts
massspectrometry
updated 9.2 years ago by
Gordon Smyth
50k • written 9.2 years ago by
Ben Neely
▴ 40
1
vote
1
reply
5.5k
views
Mfuzz: fill.NA - Warning messages: argument is not numeric or logical: returning NA
mfuzz
clustering
bioinformatics
proteomics
timecourse
updated 8.2 years ago by
Laurent Gatto
1.6k • written 8.2 years ago by
under-waterworld
• 0
1
vote
3
replies
4.8k
views
EdgeR for proteomics data
Proteomics
Normalization
edgeR
Proteomics
Normalization
edgeR
updated 18 months ago by
Divya
• 0 • written 10.3 years ago by
Phinney, Brett
▴ 10
1
vote
1
reply
4.7k
views
edgeR: pseudocounts, logConc and logFC
Proteomics
graph
edgeR
Proteomics
graph
edgeR
updated 14.1 years ago by
Mark Robinson
★ 1.1k • written 14.1 years ago by
Ann Hess
▴ 340
0
votes
0
replies
4.0k
views
Bioconductor 2.13 is released
BiocViews
aCGH
SNP
Transcription
Sequencing
miRNA
Microarray
Genetics
Proteomics
Coverage
10.5 years ago
Dan Tenenbaum
★ 8.2k
5
votes
6
replies
3.8k
views
Differential protein/biomarker expression using limma: is that possible?
Proteomics
NPX
limma
updated 3 months ago by
briankleiboeker
• 0 • written 3.1 years ago by
r.i.s.alnuwaysir
▴ 10
8
votes
0
replies
3.6k
views
Tutorial:
Statistics and Computing in Genome Science (CSAMA) Course Material
rnaseq
chipseq
visualization
metagenomics
proteomics
Tutorial
8.8 years ago
Martin Morgan
25k
0
votes
3
replies
3.3k
views
from RefSeq to GO terms / gene symbol to geneID
Proteomics
Coverage
Annotation
GO
Proteomics
Coverage
Annotation
GO
16.9 years ago • updated 16.8 years ago
Simon Lin
▴ 270
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
1
vote
6
replies
3.2k
views
DEP package: Problems installing on macOS
software error
DEP
proteomics
updated 3.8 years ago by
Laurent Gatto
1.6k • written 3.8 years ago by
jp
• 0
2
votes
1
reply
3.1k
views
Convert UniProt Entry Names into Gene Symbols
Proteomics
ProteomicsWorkflow
UniProt.ws
updated 3.2 years ago by
James W. MacDonald
65k • written 3.2 years ago by
Dario Strbenac
★ 1.5k
0
votes
0
replies
3.0k
views
PhD student in Bioinformatics, Computational Biology at Technical University of Munich, Germany
Proteomics
Pathways
Proteomics
Pathways
12.7 years ago
Amin Moghaddasi
▴ 130
3
votes
4
replies
2.9k
views
Protein differential Expression analysis
differential expression
proteomics
updated 8 months ago by
ATpoint
★ 4.0k • written 6.3 years ago by
cardin.julie
• 0
8
votes
2
replies
2.9k
views
Statistical analysis of Spectral count data : edgeR, limma or others ?
spectral counts
proteomics
limma
edger
deseq
updated 8.8 years ago by
Gordon Smyth
50k • written 8.8 years ago by
eleonoregravier
▴ 70
0
votes
1
reply
2.8k
views
Import Bam index (Rsamtools)
Proteomics
Rsamtools
Proteomics
Rsamtools
updated 12.1 years ago by
Martin Morgan
25k • written 12.1 years ago by
Francesco Mancuso
▴ 110
1
vote
2
replies
2.8k
views
Limma: technical and biological replicates in proteomics data
limma
proteomics
replicates
updated 5.7 years ago by
Aaron Lun
★ 28k • written 5.7 years ago by
ivansilbern
• 0
1
vote
5
replies
2.8k
views
Using Limma for proteomics (2D DIGE) datasets
Proteomics
limma
impute
limmaGUI
Proteomics
limma
impute
limmaGUI
updated 8.8 years ago by
sm
• 0 • written 14.5 years ago by
Tom Wenseleers
▴ 60
0
votes
1
reply
2.7k
views
GenomeViz again : corrected link
Proteomics
genomes
Proteomics
genomes
updated 19.3 years ago by
A.J. Rossini
▴ 210 • written 19.3 years ago by
Rohit Ghai
▴ 80
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
0
votes
0
replies
2.4k
views
8. CGHCall problems (Bernard North [guest]) : Bioconductor Digest, Vol 126, Issue 7
aCGH
RNASeq
ChIPSeq
Proteomics
Annotation
Normalization
GO
Network
Cancer
ChipName
probe
10.6 years ago
Sarah JugurnauthLittle
▴ 20
0
votes
3
replies
2.4k
views
How to carry out Gene Set Enrichment Analysis(GSEA) on an ordered list of Entrezgene ids?
Proteomics
hgu95av2
GSEABase
Proteomics
hgu95av2
GSEABase
15.8 years ago
anna freni sterrantino
▴ 120
2
votes
0
replies
2.3k
views
Job:
Bioconductor infrastructure for the integration of genomics, transcriptomics and proteomics data
proteomics
genomics
transcriptomics
software
Job
4.6 years ago
Laurent Gatto
1.6k
0
votes
16
replies
2.3k
views
liimma and Across Array Normalisation
Microarray
Proteomics
Microarray
Proteomics
updated 10.2 years ago by
Gordon Smyth
50k • written 10.2 years ago by
Saket Choudhary
▴ 130
0
votes
0
replies
2.3k
views
Open PhD Position - Bioinformatics in collaboration with SAP
Proteomics
Proteomics
12.0 years ago
Amin Moghaddasi
▴ 130
3
votes
1
reply
2.2k
views
Tutorial:
Mass Spectrometry Data Analysis with the Spectra Package
mass spectrometry
proteomics
metabolomics
Tutorial
written 3.5 years ago by
Johannes Rainer
★ 2.0k
3
votes
0
replies
2.2k
views
Job:
Postdoctoral Scientist, Statistical Bioinformatics and Proteomics, WEHI Australia
job
proteomics
Job
statistics
4.5 years ago • updated 4.3 years ago
Gordon Smyth
50k
0
votes
3
replies
2.2k
views
limma and Volcano Plots
Microarray
Proteomics
Cancer
PROcess
Microarray
Proteomics
Cancer
PROcess
updated 10.2 years ago by
Gordon Smyth
50k • written 10.2 years ago by
Saket Choudhary
▴ 130
4
votes
9
replies
2.2k
views
Limma is doing the right way to calculate the fold change?
limma
proteomics
updated 6.9 years ago by
Laurent Gatto
1.6k • written 6.9 years ago by
Bioinformatics
▴ 30
0
votes
0
replies
2.1k
views
Job:
Abbvie -- Senior Manager/Associate Director, Exploratory Statistics
genomics
genetics
proteomics
rnaseq
microarray
Job
9.1 years ago
Feng Hong
• 0
0
votes
5
replies
2.1k
views
Package plgem for analysis of spectral counts, was 'limma for spectral counts'
Microarray
Proteomics
limma
plgem
Microarray
Proteomics
limma
plgem
updated 13.5 years ago by
Yolande Tra
▴ 120 • written 13.5 years ago by
Pavelka, Norman
▴ 70
0
votes
3
replies
2.1k
views
Problem with XCMS
xcms
metabolomics
lipidomics
proteomics
massspectrometry
8.3 years ago
Titan
• 0
1
vote
8
replies
2.0k
views
DESEQ2 and continuous data
proteomics
deseq2
8.2 years ago
carandres74
• 0
1
vote
2
replies
2.0k
views
Errors installing mzR package
proteomics
error
updated 5.1 years ago by
Laurent Gatto
1.6k • written 5.1 years ago by
pdaltron
• 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
Laurent Gatto
1.6k • written 5.2 years ago by
fgol
▴ 10
2
votes
1
reply
2.0k
views
DESeq package
Proteomics
DESeq
Proteomics
DESeq
updated 11.5 years ago by
Bernd Fischer
▴ 550 • written 11.5 years ago by
Maia de Oliveira, Julio
▴ 20
0
votes
8
replies
2.0k
views
IPI to entrez id
Proteomics
GO
biomaRt
Proteomics
GO
biomaRt
13.1 years ago
Dick Beyer
★ 1.4k
1
vote
1
reply
2.0k
views
Job:
junior level position in proteomics/data science
proteomics
machine learning
git
docker
Job
updated 6.3 years ago by
karimse07
• 0 • written 6.6 years ago by
petyuk
▴ 70
0
votes
0
replies
2.0k
views
Post Doc position, Berlin Germany
Sequencing
Microarray
Proteomics
Pathways
Network
Cancer
Sequencing
Microarray
Proteomics
15.0 years ago
Paul Hammer
▴ 220
1
vote
0
replies
1.9k
views
News:
May Institute 2018 - Computation and statistics for mass spectrometry and proteomics at Northeastern University in Boston
bioconductor
training
course
msstats
proteomics
News
6.3 years ago
mnchoi67
▴ 40
0
votes
2
replies
1.9k
views
Job:
Postdoc bioinformatics in proteomics
proteomics
job
bioinformatics
Netherlands
Job
8.8 years ago
b.nota
▴ 360
3
votes
4
replies
1.9k
views
Enrichment Analysis for Shot-gun proteomics data using the ReactomePA package: problem with identities loss
reactomepa
reactome.db
reactome
proteomics
uniprot accessions
updated 6.5 years ago by
willem.ligtenberg
▴ 150 • written 6.5 years ago by
Miguel.Cosenza
▴ 10
0
votes
9
replies
1.8k
views
RforProteomics workflow troubleshooting
proteomics
7.8 years ago
yockpingchow
• 0
0
votes
1
reply
1.8k
views
limma/voom for protein intensity data
limma
proteomics
voom
updated 2.6 years ago by
ATpoint
★ 4.0k • written 2.6 years ago by
Endre Sebestyén
▴ 70
5
votes
3
replies
1.8k
views
Strong upwards correlation between log fold change and average log expression in MD plot of Limma
limma
proteomics
updated 6.5 years ago by
Gordon Smyth
50k • written 6.5 years ago by
gil.hornung
• 0
1
vote
2
replies
1.8k
views
Proteomics: package/statistics to compare very different LFQ-proteomes
dep
proteomics
limma
4.3 years ago
Rob
• 0
0
votes
0
replies
1.8k
views
what is the difference between iBAQ or LFQ?
Proteomics
DEP
limma
written 2.8 years ago by
barrypraveen
• 0
2
votes
5
replies
1.7k
views
proteomics analysis
Proteomics
analysis
updated 21 months ago by
jeroen.gilis
▴ 90 • written 21 months ago by
Shakiba
• 0
0
votes
3
replies
1.7k
views
GeneSetCollection from GSEA
Proteomics
GSEABase
Proteomics
GSEABase
updated 16.2 years ago by
Martin Morgan
25k • written 16.2 years ago by
Paul ChristophSchröder
▴ 70
0
votes
0
replies
1.7k
views
Differential protein abundance testing using emPAI values?
proteomics
limma
7.7 years ago
Jenny Drnevich
★ 2.0k
50 results • Page
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Answer: Dominance Index for Shotgun Metagenomics Data
by
Leo Lahti
▴ 40
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…
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Answer: Dominance Index for Shotgun Metagenomics Data
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)
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