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DESeq2 high fold change values for comparison of samples with zero counts
GO
DESeq2
GO
DESeq2
12.0 years ago
Michael Love
43k
0
votes
2
replies
1.3k
views
multiple groups time course RNA Seq LIMMA
limma
limma
updated 12.0 years ago by
Gordon Smyth
53k • written 12.0 years ago by
Riba Michela
▴ 40
0
votes
1
reply
1.1k
views
question edgeR multifactorial design
edgeR
updated 3.1 years ago by
Gordon Smyth
53k • written 12.0 years ago by
David R
▴ 90
0
votes
1
reply
2.0k
views
[MEDIPS] mergeFrames: `Error in rbind(output, cbind(chromosomes[i], new_start, new_stop)) `
Coverage
Regression
edgeR
MEDIPS
Coverage
Regression
edgeR
MEDIPS
updated 12.0 years ago by
Matthias Lienhard
▴ 280 • written 12.0 years ago by
Pierre Lindenbaum
▴ 10
0
votes
1
reply
3.7k
views
GLM common and trended dispersion EdgeR
edgeR
edgeR
updated 12.0 years ago by
Reema Singh
▴ 570 • written 12.0 years ago by
Gordon Smyth
53k
0
votes
1
reply
1.9k
views
estimating size factors in DESeq produces warnings
DESeq
DESeq
updated 12.0 years ago by
Simon Anders
★ 3.8k • written 12.0 years ago by
Assa Yeroslaviz
★ 1.5k
0
votes
3
replies
2.6k
views
ChIPpeakAnno: TSS at - strand
Annotation
convert
ChIPpeakAnno
Annotation
convert
ChIPpeakAnno
12.0 years ago
Julie Zhu
★ 4.3k
0
votes
1
reply
1.7k
views
I need help making a dcf seed file to encapsulate a genome assembly im using.
Cancer
Yeast
BSgenome
BSgenome
Cancer
Yeast
BSgenome
BSgenome
updated 12.0 years ago by
ashteyma@andrew.cmu.edu
▴ 10 • written 12.0 years ago by
Hervé Pagès
16k
0
votes
2
replies
2.4k
views
help with analysis of genotyping data from Illumina HumanOmni5-4v1_B chip
SNP
Annotation
SNP
Annotation
updated 12.0 years ago by
Stephanie M. Gogarten
▴ 890 • written 12.0 years ago by
Abhishek Pratap
▴ 190
0
votes
9
replies
3.1k
views
using frma and brainarray cdf on exon arrays
cdf
affy
PROcess
oligo
xps
frma
cdf
affy
PROcess
oligo
xps
frma
updated 12.0 years ago by
Stephen Piccolo
▴ 600 • written 12.0 years ago by
Ty Thomson
▴ 100
0
votes
4
replies
2.0k
views
AllelicImbalance with VCFs?
RNASeq
Cancer
trio
AllelicImbalance
RNASeq
Cancer
trio
AllelicImbalance
updated 12.0 years ago by
Jesper Robert Gadin
▴ 20 • written 12.0 years ago by
Tim Triche, Jr.
▴ 10
0
votes
1
reply
2.0k
views
retrieving LD between two known SNPs with rsID
biomaRt
biomaRt
updated 12.0 years ago by
Valerie Obenchain
★ 6.8k • written 12.0 years ago by
Lescai, Francesco
▴ 380
0
votes
1
reply
803
views
extracting transcripts
edgeR
edgeR
updated 12.0 years ago by
James W. MacDonald
68k • written 12.0 years ago by
Jahn Davik
▴ 110
0
votes
1
reply
1.7k
views
Statistics questions regarding the use of Ambion ExFold ERCC standards with Affmetrix ST arrays.
Normalization
vsn
graph
Normalization
vsn
graph
updated 12.0 years ago by
James W. MacDonald
68k • written 12.0 years ago by
Matthew Thornton
▴ 390
1
vote
3
replies
6.2k
views
EdgeR for proteomics data
Proteomics
Normalization
edgeR
Proteomics
Normalization
edgeR
updated 3.3 years ago by
Divya
• 0 • written 12.0 years ago by
Phinney, Brett
▴ 10
0
votes
0
replies
1.3k
views
An introductory course to RNA-seq at MBC Via Nizza 52, Torino, Italy, 25-27 March 2014
RNASeq
RNASeq
12.0 years ago
raffaele calogero
▴ 500
0
votes
2
replies
3.0k
views
ensemblVEP, variant_effect_predictor versions and release schedule
Transcription
HapMap
PolyPhen
SIFT
convert
genomes
ensemblVEP
Transcription
HapMap
SIFT
updated 12.0 years ago by
Valerie Obenchain
★ 6.8k • written 12.0 years ago by
Thomas Sandmann
▴ 30
0
votes
3
replies
2.2k
views
EdgeR design question?
edgeR
edgeR
updated 12.0 years ago by
Gordon Smyth
53k • written 12.0 years ago by
joseph
▴ 330
0
votes
0
replies
681
views
[job offer phd position]
12.0 years ago
Guest User
★ 13k
0
votes
3
replies
2.0k
views
'xps' package installation fails with ROOT installed from the Ubuntu (13.10) repositories
updated 12.0 years ago by
cstrato
★ 3.9k • written 12.0 years ago by
Barry Garchow
▴ 20
0
votes
1
reply
3.4k
views
limma - normalizeBetweenArrays function
Microarray
limma
Microarray
limma
updated 12.0 years ago by
Gordon Smyth
53k • written 12.0 years ago by
MIKE STARKEY
▴ 10
0
votes
7
replies
4.9k
views
Q-values way smaller than P-values! Is that kosher?
qvalue
qvalue
updated 12.0 years ago by
Michael Love
43k • written 12.0 years ago by
Joshua Banta
▴ 30
0
votes
1
reply
1.2k
views
Best way to remove noise from dataset.
updated 12.0 years ago by
Arnar Flatberg
▴ 70 • written 12.0 years ago by
Fenton Christopher Graham
▴ 90
0
votes
1
reply
1.4k
views
EdgeR multi-factor testing question
updated 12.0 years ago by
Gordon Smyth
53k • written 12.0 years ago by
Guest User
★ 13k
0
votes
2
replies
1.6k
views
DESeq nbinomGLMTest specific comparisons
DESeq
DESeq2
DESeq
DESeq2
updated 12.0 years ago by
Ryan C. Thompson
★ 7.9k • written 12.0 years ago by
James Floyd
▴ 40
1
vote
1
reply
8.6k
views
biomaRt: retrieve exon sequence, start and end positions
updated 12.0 years ago by
Steffen Durinck
▴ 540 • written 12.0 years ago by
Tim Smith
★ 1.1k
0
votes
0
replies
2.1k
views
R pathview and mouse
Category
pathview
Category
pathview
12.0 years ago
Luo Weijun
★ 1.6k
0
votes
3
replies
2.6k
views
annotation of a probe in hgu133plus2
Annotation
Annotation
updated 12.0 years ago by
James W. MacDonald
68k • written 12.0 years ago by
Mayte Suarez-Farinas
▴ 510
0
votes
7
replies
1.4k
views
Annotate package not working
updated 12.0 years ago by
James W. MacDonald
68k • written 12.0 years ago by
Ryan C. Thompson
★ 7.9k
0
votes
5
replies
2.5k
views
GLM common and trended dispersion EdgeR.
edgeR
edgeR
12.0 years ago
Reema Singh
▴ 570
0
votes
0
replies
1.2k
views
diffbind question : bSubControl with DEseq
DESeq
DiffBind
DESeq
DiffBind
12.0 years ago
Rory Stark
★ 5.2k
0
votes
0
replies
771
views
Question about best analysis method for a complex array experiment design
limma
limma
12.0 years ago
Gordon Smyth
53k
0
votes
2
replies
1.7k
views
Gviz UcscTrack error
updated 12.0 years ago by
florian.hahne@novartis.com
★ 1.6k • written 12.0 years ago by
Guest User
★ 13k
0
votes
1
reply
839
views
Multi-level experiments
limma
limma
updated 12.0 years ago by
Dario Strbenac
★ 1.6k • written 12.0 years ago by
Guest User
★ 13k
0
votes
1
reply
1.2k
views
package installation
gCMAPWeb
gCMAPWeb
updated 12.0 years ago by
James W. MacDonald
68k • written 12.0 years ago by
array chip
▴ 420
0
votes
0
replies
1.9k
views
EximiR - Limma - miRCURY LNA - Exiqon
miRNA
Microarray
Cancer
limma
lumi
ExiMiR
miRNA
Microarray
Cancer
limma
lumi
ExiMiR
12.0 years ago
Paolo Kunderfranco
▴ 350
0
votes
0
replies
1.5k
views
Question about best analysis method for a complex array expriment design
limma
limma
12.0 years ago
Agnes Paquet
▴ 30
0
votes
2
replies
1.0k
views
BiocStyle short header
updated 12.0 years ago by
Martin Morgan
25k • written 12.0 years ago by
Andrzej Oleś
▴ 750
0
votes
2
replies
2.1k
views
VCF as custom variant annotation database
Annotation
SNPlocs
Annotation
SNPlocs
updated 12.0 years ago by
Valerie Obenchain
★ 6.8k • written 12.0 years ago by
Lescai, Francesco
▴ 380
0
votes
1
reply
1.0k
views
EdgeR multi-factor testing questions
RNASeq
edgeR
RNASeq
edgeR
updated 12.0 years ago by
Gordon Smyth
53k • written 12.1 years ago by
Guest User
★ 13k
0
votes
1
reply
807
views
Retrieving Adjusted Individual Channel Intensities
limma
limma
updated 12.0 years ago by
James W. MacDonald
68k • written 12.0 years ago by
Guest User
★ 13k
0
votes
0
replies
1.0k
views
EdgeR multi-fact� or testing questions
12.0 years ago
Guest User
★ 13k
0
votes
2
replies
1.3k
views
miRBase
updated 12.0 years ago by
Shantanu Karkare
▴ 10 • written 12.1 years ago by
Guest User
★ 13k
2
votes
5
replies
4.0k
views
Problem with BAM header in GAlignments
Cancer
Cancer
updated 12.0 years ago by
Martin Morgan
25k • written 12.0 years ago by
Taylor, Sean D
▴ 250
0
votes
1
reply
1.1k
views
Most efficient way to compute width of overlap of multiple features
GenomicRanges
GenomicRanges
updated 12.0 years ago by
Michael Lawrence
★ 11k • written 12.0 years ago by
Charles Berry
▴ 290
1
vote
1
reply
4.2k
views
Most efficient way to compute width of overlap of multiple features
updated 12.0 years ago by
Michael Lawrence
★ 11k • written 12.0 years ago by
Charles Berry
▴ 290
1
vote
6
replies
3.6k
views
DESeq2 high fold change values for comparison of samples with zero counts
DESeq2
DESeq2
updated 12.0 years ago by
Michael Love
43k • written 12.0 years ago by
Noa Henig
▴ 60
0
votes
13
replies
3.5k
views
Extracting protein sequence associated to UCSC transcript id
updated 12.0 years ago by
Michael Lawrence
★ 11k • written 12.0 years ago by
rcaloger
▴ 500
0
votes
0
replies
1.6k
views
Job opening: Staff Scientist – Computational Biology and Bioinformatics – Massachusetts General Hospital, Boston, MA, USA
Sequencing
Microarray
Cancer
Sequencing
Microarray
Cancer
12.0 years ago
Wittner, Ben
▴ 290
0
votes
0
replies
837
views
Most efficient way to compute width of overlap of multiple features
12.0 years ago
Vince S. Buffalo
▴ 140
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Comment: Combining two proteomics datasets with limpa
by
Andrew Pattison
• 0
Thanks heaps Gordon. I went with option 1 and no normalisation and all seems to have worked well. Cheers, Andrew
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry
by
Gordon Smyth
53k
Flagging protein groups as likely contaminants in this way will be fine for a limpa analysis. The `Cont_` proteins can optionally stay in f…
Answer: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
Gordon Smyth
53k
Aaron Lun was a PhD student in my Lab back in 2015, when he posted the answers about allele-specific expression that you and Mike Love have…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
Michael Love
43k
You just need the mouse identifier (controls baseline) and the group specific allelic effect.
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry
by
Julia Broadbent
• 0
Hi Emily, Just sharing a resource for handling contaminants - we use the methods described in [Frankenfield et al. (2022)](https://pubs.acs…
Votes
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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