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[devteam-bioc] Depth of Coverage and Base counts from BAM file
Coverage
Cancer
Rsamtools
Coverage
Cancer
Rsamtools
12.4 years ago
Hervé Pagès
16k
0
votes
0
replies
2.0k
views
Change enzyme code (EC) into gene symbol
Pathways
graph
pathview
Pathways
graph
pathview
12.4 years ago
Luo Weijun
★ 1.6k
0
votes
1
reply
1.2k
views
MEDIPS saturation error
Alignment
BSgenome
BSgenome
MEDIPS
Alignment
BSgenome
BSgenome
MEDIPS
updated 12.4 years ago by
Sara Castelletti
▴ 40 • written 12.4 years ago by
Guest User
★ 13k
0
votes
6
replies
2.2k
views
How does one deal with spatial effects detected on single channel microarrays?
Microarray
Normalization
affy
marray
nnNorm
Microarray
Normalization
affy
marray
nnNorm
updated 12.4 years ago by
cstrato
★ 3.9k • written 12.4 years ago by
Guest User
★ 13k
12
votes
3
replies
5.8k
views
sva: how to incorporate adjusting variables
inveRsion
sva
inveRsion
sva
updated 12.4 years ago by
Jeff Leek
▴ 650 • written 12.4 years ago by
Meritxell Oliva
▴ 120
0
votes
1
reply
1.9k
views
Can I input ordinal variables into a model in Limma?
Microarray
limma
Microarray
limma
updated 12.4 years ago by
Scott Robinson
▴ 130 • written 12.4 years ago by
Gordon Smyth
53k
0
votes
0
replies
1.7k
views
microarray outlier detection
Microarray
limma
Microarray
limma
12.4 years ago
Gordon Smyth
53k
0
votes
1
reply
1.6k
views
XPS package QC data
affy
arrayQualityMetrics
xps
affy
arrayQualityMetrics
xps
12.4 years ago
cstrato
★ 3.9k
0
votes
1
reply
1.2k
views
predFC doesn't use norm factors?
Normalization
Normalization
updated 12.4 years ago by
Gordon Smyth
53k • written 12.4 years ago by
Jenny Drnevich
★ 2.0k
0
votes
2
replies
2.4k
views
microarray outlier detection
Microarray
Microarray
updated 12.4 years ago by
Devon Ryan
▴ 200 • written 12.4 years ago by
Guest User
★ 13k
0
votes
6
replies
1.9k
views
download packages VariantTools
VariantTools
VariantTools
updated 12.4 years ago by
Dan Tenenbaum
★ 8.2k • written 12.4 years ago by
francesca bergantino
▴ 30
0
votes
1
reply
1.4k
views
Differential expression analysis in Limma for one factor after adjusting for a covariate
limma
limma
updated 12.4 years ago by
James W. MacDonald
68k • written 12.4 years ago by
QAMRA Aditi GIS
▴ 120
0
votes
1
reply
1.8k
views
topGO analysis returns different gene counts for category than given for non-model organism
GO
Category
topGO
GO
Category
topGO
updated 12.4 years ago by
Valerie Obenchain
★ 6.8k • written 12.4 years ago by
Diana Toups Dugas
▴ 20
0
votes
2
replies
1.7k
views
DEseq for paired samples
updated 12.4 years ago by
Devon Ryan
▴ 200 • written 12.4 years ago by
Prabhakar Chalise
▴ 10
0
votes
0
replies
926
views
Can I input ordinal variables into a model in Limma?
Microarray
limma
Microarray
limma
12.4 years ago
Guest User
★ 13k
0
votes
0
replies
1.6k
views
Job in GWAS / Next Gen Sequencing / genetics
Sequencing
Genetics
Sequencing
Genetics
12.4 years ago
Paul Leo
▴ 970
0
votes
1
reply
891
views
Genes, their domains, and a list of superimposed mutations
updated 12.4 years ago by
Martin Morgan
25k • written 12.4 years ago by
Guest User
★ 13k
0
votes
0
replies
3.4k
views
DiffBind questions
Transcription
Cancer
DiffBind
MMDiff
Transcription
Cancer
DiffBind
MMDiff
12.4 years ago
Rory Stark
★ 5.2k
0
votes
0
replies
742
views
EdgeR
edgeR
edgeR
12.4 years ago
Gordon Smyth
53k
0
votes
0
replies
1.6k
views
Chr Info for array CGH - agilent 60K
CGH
CGH
12.4 years ago
Cian Murphy
▴ 40
0
votes
0
replies
941
views
confusing P-value of one gene
edgeR
edgeR
12.4 years ago
Gordon Smyth
53k
0
votes
1
reply
1.2k
views
tweeDEseq glm reduced model specification?
tweeDEseq
tweeDEseq
updated 12.4 years ago by
Gonzalez Ruiz, Juan Ramon
▴ 20 • written 12.4 years ago by
Ryan C. Thompson
★ 7.9k
0
votes
5
replies
1.8k
views
Mapping Affymetrix annotations with Bioconductor annotations
updated 12.4 years ago by
James W. MacDonald
68k • written 12.4 years ago by
Joao Sollari Lopes
▴ 80
0
votes
1
reply
1.6k
views
Depth of Coverage and Base counts from BAM file
updated 12.4 years ago by
Julian Gehring
★ 1.3k • written 12.4 years ago by
Guest User
★ 13k
0
votes
5
replies
2.7k
views
Change enzyme code (EC) into gene symbol
updated 12.4 years ago by
Luo Weijun
★ 1.6k • written 12.4 years ago by
Ed
▴ 230
0
votes
2
replies
3.1k
views
BiomaRt and archival versions of ensembl_mart
biomaRt
biomaRt
updated 12.4 years ago by
Steffen Durinck
▴ 540 • written 12.4 years ago by
Greg Slodkowicz
▴ 50
0
votes
0
replies
782
views
Error while background correction
GO
probe
GO
probe
12.4 years ago
kunal jha
▴ 10
0
votes
3
replies
4.3k
views
EdgeR: getting CPM values after batch effect correction
edgeR
edgeR
updated 12.4 years ago by
Ryan C. Thompson
★ 7.9k • written 12.4 years ago by
Gilgi Friedlander
▴ 90
0
votes
0
replies
1.5k
views
Annotating Results for HuEx 1.0 STv2 - Oligo
annotate
oligo
annotate
oligo
12.4 years ago
Bade
▴ 310
0
votes
0
replies
1.3k
views
tweeDEseq main paper
edgeR
tweeDEseq
edgeR
tweeDEseq
12.4 years ago
Gonzalez Ruiz, Juan Ramon
▴ 20
0
votes
0
replies
1.7k
views
Gene Vs Transcript level Differential expression analysis
edgeR
Rsubread
edgeR
Rsubread
12.4 years ago
Alan Smith
▴ 150
0
votes
0
replies
1.1k
views
question on ChIPpeakAnno::getEnrichedGO
GO
ChIPpeakAnno
GO
ChIPpeakAnno
12.4 years ago
Julie Zhu
★ 4.3k
0
votes
5
replies
2.1k
views
Finding my un-counted reads
Sequencing
rtracklayer
ShortRead
GenomicRanges
Sequencing
rtracklayer
ShortRead
updated 12.4 years ago by
Valerie Obenchain
★ 6.8k • written 12.4 years ago by
Sam McInturf
▴ 300
0
votes
0
replies
844
views
beadarray\'s processSwathData for HumanHT12v4, with 3 swaths
12.4 years ago
Guest User
★ 13k
0
votes
0
replies
934
views
enrichment packages that accept t-stat (or related stat) as input
limma
gage
limma
gage
12.4 years ago
Luo Weijun
★ 1.6k
0
votes
6
replies
1.9k
views
minfi: control probes sequence
Annotation
Annotation
updated 12.4 years ago by
Tim Triche
★ 4.2k • written 12.4 years ago by
Rohmatul Fajriyah
▴ 190
0
votes
4
replies
5.0k
views
Problem reading Cel files - Oligo Package
Annotation
oligo
Annotation
oligo
updated 12.4 years ago by
James W. MacDonald
68k • written 12.4 years ago by
Bade
▴ 310
0
votes
3
replies
2.3k
views
edgeR topTags output (logFC)
edgeR
edgeR
updated 12.4 years ago by
Gordon Smyth
53k • written 12.4 years ago by
Guest User
★ 13k
2
votes
0
replies
2.3k
views
Complex Limma design: technical replication, biological replication and repeated experiment
Microarray
limma
Microarray
limma
12.4 years ago
Gordon Smyth
53k
0
votes
0
replies
1.1k
views
Job: Bioinformatician (m/f) Core Facility - Mainz, Germany
12.4 years ago
Holger Klein
▴ 20
0
votes
1
reply
869
views
import only partial samples of an array
updated 12.4 years ago by
Pan Du
▴ 440 • written 12.4 years ago by
Guest User
★ 13k
0
votes
0
replies
772
views
edgeR
edgeR
edgeR
12.4 years ago
Joanne.Lee@csiro.au
▴ 10
0
votes
2
replies
1.5k
views
'version' is missing error when running makeTxDbPackageFromUCSC
TranscriptDb
IRanges
TranscriptDb
IRanges
updated 12.4 years ago by
Dan Tenenbaum
★ 8.2k • written 12.4 years ago by
Michael Steeves
▴ 40
0
votes
0
replies
1.3k
views
Package/Function for Single Channel Microarray Spatial Normalization?
marray
OLIN
marray
OLIN
12.4 years ago
Guest User
★ 13k
0
votes
0
replies
2.6k
views
makeTranscriptDbFromGFF fails on NCBI Bacteria
Alignment
Annotation
Normalization
GO
Preprocessing
Clustering
Cancer
Organism
probe
GLAD
12.4 years ago
Sarah Pohl
▴ 30
0
votes
1
reply
740
views
Hello, reading large Affymetrix microarrays .CEL files
updated 12.4 years ago by
Steve Lianoglou
★ 13k • written 12.4 years ago by
Nehme Hachem
▴ 20
0
votes
1
reply
1.7k
views
Using the genes.count-tracking file from cuffdiff in DESeq
DESeq
DESeq
updated 12.4 years ago by
Michael Love
43k • written 12.4 years ago by
Guest User
★ 13k
1
vote
0
replies
1.7k
views
Fwd: GViz trouble retreiving X chromosome data with BiomartGeneRegionTrack
Annotation
ideogram
Gviz
Annotation
ideogram
Gviz
12.4 years ago
Martin Rijlaarsdam
▴ 190
0
votes
1
reply
1.5k
views
Reg: makePdInfoPackage Error in sqliteExecStatement(con, statement, bind.data) : bind.data must have non-zero dimensions
Annotation
PROcess
pdInfoBuilder
charm
Annotation
PROcess
pdInfoBuilder
charm
12.4 years ago
Nitesh Turaga
▴ 50
0
votes
0
replies
887
views
confusing P-value (from egdeR) of one gene
edgeR
edgeR
12.4 years ago
Xinwei Han
▴ 30
46,711 results • Page
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Comment: Ensembl plants at annotationHub?
by
jwp48
• 0
Nope I don't mind haha! Anyway thanks so much! Thats super kind of you!
Answer: Combining two proteomics datasets with limpa
by
Gordon Smyth
53k
Hi Andrew, We don't have that much experience combining different datasets with limpa yet, but my feeling is that the same DPC should be u…
Comment: Guitar R package requires update due to dependency GenomicFeatures
by
ferran.llobet.cabau
▴ 10
Thank you @seandavi for your feedback. I followed your recommendations and generated a [pull request][1] including the fix for this issue…
Comment: Ensembl plants at annotationHub?
by
Guido Hooiveld
★ 4.1k
Hope you don't mind I am not Johannes... ;-) Note that you nowadays can generate these yourselves using the `docker` image Johannes made av…
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in
by
jtsy6383
• 0
Thanks for the reminder about DiffVar (for that project I ended up using GAMLSS in the end and haven't touched DiffVar since) and the alter…
Votes
A: What is logFC and "B" in methylation analysis ??
limma moderated t-statistics and B-statistics
Comment: Guitar R package requires update due to dependency GenomicFeatures
A: how to control age and gender effect in expression data using DESeq2
A: how to control age and gender effect in expression data using DESeq2
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