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replies
1.1k
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BiomaRt returns empty set for getBM for celegans miRNA
biomaRt
biomaRt
13.7 years ago
Julie Zhu
★ 4.3k
0
votes
1
reply
903
views
BSgenome.Ggallus.UCSC.galGal3 missing chromosomes?
updated 13.7 years ago by
Hervé Pagès
16k • written 13.7 years ago by
Martin Johnsson
▴ 10
0
votes
10
replies
5.0k
views
edgeR outlier question
RNASeq
edgeR
RNASeq
edgeR
updated 13.7 years ago by
Gordon Smyth
53k • written 13.7 years ago by
Simon Melov
▴ 340
0
votes
3
replies
1.8k
views
Building specific Ortoghonal contrasts in LIMMA
limma
gcrma
limma
gcrma
updated 13.7 years ago by
Gordon Smyth
53k • written 13.7 years ago by
Garcia Orellana,Miriam
▴ 150
0
votes
1
reply
1.1k
views
Random Forest Code
updated 13.7 years ago by
Moshe Olshansky
▴ 260 • written 13.7 years ago by
Bahar AZ
▴ 10
0
votes
2
replies
1.4k
views
EdgeR exactTest - treatment names determine sign of fold change
edgeR
edgeR
updated 13.7 years ago by
Mark Robinson
▴ 880 • written 13.7 years ago by
Spollen, William G.
▴ 30
0
votes
1
reply
2.0k
views
How to use DESeq output to convert raw counts to normalized data
convert
DESeq
convert
DESeq
updated 13.7 years ago by
Simon Anders
★ 3.8k • written 13.7 years ago by
Xin Davis
▴ 30
0
votes
2
replies
3.4k
views
Problem using biomaRt to retrieve human SNPs given a list of gene symbols
biomaRt
biomaRt
updated 13.7 years ago by
ying chen
▴ 340 • written 13.7 years ago by
Yong Li
▴ 80
0
votes
0
replies
1.5k
views
FOSBE 2012
SANTA
SANTA
13.7 years ago
mabawsa
▴ 20
0
votes
9
replies
2.2k
views
How to use DESeq to normalize and estimate variance in a RNAseq timecourse analysis
Normalization
DESeq
Normalization
DESeq
updated 13.7 years ago by
Wolfgang Huber
★ 13k • written 13.7 years ago by
Marie Sémon
▴ 50
0
votes
11
replies
1.8k
views
v is for values()
updated 13.7 years ago by
Steve Lianoglou
★ 13k • written 13.7 years ago by
Tim Triche
★ 4.2k
0
votes
9
replies
4.0k
views
Moderated t-test
updated 13.7 years ago by
Gordon Smyth
53k • written 13.7 years ago by
Chintanu
▴ 310
0
votes
0
replies
1.2k
views
Outcome~predictor model evaluation, repeated measurements
Regression
Regression
13.7 years ago
rad mac
▴ 10
0
votes
5
replies
2.0k
views
Human Illumina Methylation27k question
updated 13.7 years ago by
Pan Du
▴ 440 • written 13.7 years ago by
Juan Fernández Tajes
▴ 190
0
votes
6
replies
2.5k
views
eset -Affy Mouse Gene 1.0 ST. Array-
affy
affy
updated 13.7 years ago by
James W. MacDonald
68k • written 13.7 years ago by
alessandro brozzi
▴ 120
0
votes
0
replies
2.6k
views
Open PhD Position - Bioinformatics in collaboration with SAP
Proteomics
Proteomics
13.7 years ago
Amin Moghaddasi
▴ 130
0
votes
1
reply
865
views
GO analysis for CNVs
GO
GO
updated 13.7 years ago by
Julie Zhu
★ 4.3k • written 13.7 years ago by
Yadav Sapkota
▴ 130
0
votes
0
replies
1.2k
views
DESeq Package Questions
Network
edgeR
DESeq
Network
edgeR
DESeq
13.7 years ago
Xin Davis
▴ 30
0
votes
2
replies
2.1k
views
Limma: Top 10% gene list based on p-values
limma
limma
13.7 years ago
Voke AO
▴ 760
0
votes
0
replies
2.0k
views
R / Maanova: contrasts for interaction in model with 2 fixed factors
maanova
maanova
13.7 years ago
V. Oostra
▴ 30
0
votes
1
reply
916
views
BSgenome packages for ce10 and panTro3 (was Re: BSgenome.Celegans.UCSC.cd10 for WS220)
Cancer
BSgenome
BSgenome
Cancer
BSgenome
BSgenome
updated 13.7 years ago by
Julie Zhu
★ 4.3k • written 13.7 years ago by
Hervé Pagès
16k
0
votes
2
replies
1.9k
views
normalize.AffyBatch.vsn with reference vsn object
vsn
vsn
updated 13.7 years ago by
Wolfgang Huber
★ 13k • written 13.7 years ago by
R Tagett
▴ 30
0
votes
3
replies
2.2k
views
How can I remove control probesets from the expressionset object in gene expression analysis with Affy Human Gene 1.0ST microarray
Microarray
Annotation
Normalization
GO
probe
genefilter
affy
limma
oligo
Microarray
GO
updated 13.7 years ago by
Juan Fernández Tajes
▴ 190 • written 13.7 years ago by
James W. MacDonald
68k
0
votes
6
replies
2.3k
views
outlier probes detection
hgu133plus2
hgu133plus2
updated 13.7 years ago by
Djork Clevert
▴ 210 • written 13.7 years ago by
Andrea Grilli
▴ 240
0
votes
3
replies
2.3k
views
Top 10% of genes based on p-value in TopTable
limma
limma
13.7 years ago
Voke AO
▴ 760
0
votes
2
replies
1.3k
views
question about BSgenome and C.pombe genome, absent in USCS
Cancer
BSgenome
BSgenome
Cancer
BSgenome
BSgenome
updated 13.7 years ago by
Henry Paik
▴ 30 • written 13.7 years ago by
Hervé Pagès
16k
0
votes
0
replies
1.0k
views
[Bioc-devel] technical and biological replicates in the same Exprset - Agi4x44
Microarray
Normalization
Microarray
Normalization
13.7 years ago
James W. MacDonald
68k
0
votes
2
replies
1.3k
views
FW: miRNA annotation
miRNA
Annotation
GO
Cancer
miRNA
Annotation
GO
Cancer
updated 13.7 years ago by
James W. MacDonald
68k • written 13.7 years ago by
Wu, Huiyun
▴ 70
0
votes
9
replies
2.8k
views
R IDE editor
GUI
GUI
updated 13.7 years ago by
Aaron Brandes
▴ 10 • written 13.8 years ago by
Yue Li
▴ 370
0
votes
2
replies
1.3k
views
Re-send directly to BioC on miRNA annoation
miRNA
Annotation
Cancer
miRNA
Annotation
Cancer
updated 13.7 years ago by
Valerie Obenchain
★ 6.8k • written 13.7 years ago by
Wu, Huiyun
▴ 70
0
votes
1
reply
1.4k
views
How can I remove control probesets from the expressionset object in gene expression analysis with Affy Human Gene 1.0ST microarray
Microarray
Normalization
probe
genefilter
limma
oligo
Microarray
Normalization
probe
updated 13.7 years ago by
James W. MacDonald
68k • written 13.7 years ago by
Juan Fernández Tajes
▴ 190
0
votes
1
reply
949
views
BSgenomes and protein sequences: protein names
GO
GO
updated 13.7 years ago by
Valerie Obenchain
★ 6.8k • written 13.7 years ago by
Zybaylov, Boris L
▴ 30
0
votes
3
replies
1.7k
views
export a GappedAlignment object to a BAM file
convert
convert
updated 13.7 years ago by
Michael Lawrence
★ 11k • written 13.7 years ago by
Yue Li
▴ 370
0
votes
2
replies
1.0k
views
how to unlist a list of GappedAlignments objects
updated 13.7 years ago by
Steve Lianoglou
★ 13k • written 13.7 years ago by
Yue Li
▴ 370
0
votes
3
replies
1.3k
views
miRNA annotation
Annotation
Annotation
updated 13.7 years ago by
Steve Lianoglou
★ 13k • written 13.7 years ago by
Wu, Huiyun
▴ 70
0
votes
3
replies
1.5k
views
FDR calculation for expression array
updated 13.7 years ago by
wenhuo hu
▴ 200 • written 13.7 years ago by
JiangZhengyu
▴ 40
0
votes
7
replies
3.4k
views
LIMMA: plotMDS
updated 2.5 years ago by
Gordon Smyth
53k • written 13.7 years ago by
Kripa R
▴ 180
0
votes
0
replies
2.9k
views
gene set enrichment analysis of RNA-Seq data
Microarray
limma
GLAD
edgeR
goseq
Microarray
limma
GLAD
edgeR
goseq
13.7 years ago
Paolo Guarnieri
▴ 20
0
votes
0
replies
3.1k
views
How do I find up and down regulated genes for each contrast in LIMMA?
limma
limma
13.7 years ago
Gordon Smyth
53k
0
votes
5
replies
1.4k
views
basics of GLMFit
updated 13.7 years ago by
Gordon Smyth
53k • written 13.8 years ago by
chris Jhon
▴ 260
0
votes
3
replies
13k
views
Convert gene symbols to ensembl id
convert
convert
updated 13.7 years ago by
Fred Boehm
▴ 20 • written 13.7 years ago by
michelle_low
▴ 50
0
votes
0
replies
894
views
question regarding ChIPPeakAnno use
13.7 years ago
Julie Zhu
★ 4.3k
0
votes
1
reply
831
views
how to get plant taxonomy
updated 13.7 years ago by
Wang, Li
▴ 180 • written 13.7 years ago by
wang peter
★ 2.0k
0
votes
1
reply
4.2k
views
KEGG pathway heat map
mouse4302
limma
mouse4302
limma
updated 13.7 years ago by
Felipe Antonio Riveroll Aguirre
▴ 10 • written 13.8 years ago by
Felipe Riveroll Aguirre
▴ 30
0
votes
0
replies
761
views
problem with makeFeatureDbFromUCSC and snp135Common track
13.7 years ago
Tim Triche
★ 4.2k
0
votes
1
reply
1.2k
views
NuIDs not found
Annotation
convert
minfi
Annotation
convert
minfi
updated 13.7 years ago by
Tim Triche
★ 4.2k • written 13.7 years ago by
Ed Siefker
▴ 230
0
votes
2
replies
2.0k
views
minfi -- now what?
probe
minfi
probe
minfi
updated 13.8 years ago by
Tim Triche
★ 4.2k • written 13.8 years ago by
Ed Siefker
▴ 230
0
votes
0
replies
1.2k
views
Question regarding MADE4 graphs
Cancer
made4
Cancer
made4
13.8 years ago
Aedin Culhane
▴ 510
0
votes
13
replies
3.6k
views
LIMMA decideTests result zero from contrast matrix
limma
limma
13.8 years ago
Ekta Jain
▴ 370
0
votes
0
replies
1.1k
views
normalize GFP expression by cell size and graph with densityplot
graph
graph
13.8 years ago
Chandra Jack
▴ 90
46,737 results • Page
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Answer: DESeq2 for 16S rRNA Analysis
by
James W. MacDonald
68k
The Wald test is only meant for comparison of two groups at a time, so it depends on what you mean by 'analyze across multiple groups at a …
Comment: MetaDE.pvalue: Error in xj[i]: invalid subscript type 'list'
by
varying.mastodon.isyn
• 0
Oh, that error! I remember wrestling with that one for hours when I was first learning Python. Turns out I was trying to use a list itself …
Comment: Confirm that OpenStats will not be archived (pryr dependency)
by
Marina
• 0
Thank you!
Comment: AnnotationForge makeOrgPackage rsqlite_send_query error
by
ansley.r.burtch
• 0
Hi! I am sure you are well into your career now and haven't worked on this for a while, but I wanted to let you know this is still helping …
Comment: limpa analysis advice
by
Gordon Smyth
53k
I prefer for limpa to work on precursor intensities, because my understanding is that precursors are the basic unit of identification and q…
Votes
A: DESeq2 - VST eliminates zero values
Comment: Normalise to a housekeeping gene in DESEq2
Comment: limpa analysis advice
C: AnnotationForge makeOrgPackage rsqlite_send_query error
Answer: Limpa Pipeline Order
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