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0
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9
replies
1.8k
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Re: Manova nuances
Microarray
Cancer
Microarray
Cancer
20.5 years ago
Baker, Stephen
▴ 160
0
votes
12
replies
3.5k
views
Understanding limma, fdr and topTable
Microarray
GO
limma
Microarray
GO
limma
updated 15.9 years ago by
Robson, Samuel
▴ 10 • written 15.9 years ago by
Louisa A Rispoli/AS/EXP/UTIA
▴ 160
1
vote
13
replies
5.3k
views
'Codetools' and 'mgcv' packages fail to update
package updates
codetools
deseq
mgcv
updated 9.1 years ago by
rodrigo_sengo
• 0 • written 9.2 years ago by
pbhamidipati
• 0
1
vote
6
replies
2.2k
views
SGSeq error on analyzeFeatures
SGSeq
analyzeFeatures
Splicing
9.4 years ago
Paolo Guarnieri
▴ 20
2
votes
8
replies
2.6k
views
read.FCS fails on BioRad FCS files
flowCore
8.7 years ago • updated 8.6 years ago
Robert Baer
▴ 70
16
votes
9
replies
6.6k
views
Diffbind: edgeR or DESeq2 ?
diffbind
medip-seq
edger
deseq2
updated 6.6 years ago by
Rory Stark
★ 5.2k • written 8.2 years ago by
florian.noack
▴ 60
8
votes
16
replies
3.2k
views
matrix transposing in R
affy mas5
updated 8.9 years ago by
arfranco
▴ 130 • written 8.9 years ago by
Angel
▴ 40
0
votes
6
replies
2.2k
views
HTqPCR
qPCR
GO
GLAD
HTqPCR
qPCR
GO
GLAD
HTqPCR
updated 11.9 years ago by
Heidi Dvinge
★ 2.0k • written 11.9 years ago by
Heidi Dvinge
▴ 40
1
vote
10
replies
3.0k
views
ShortRead with large fastq files
shortread
9.0 years ago
danova_fr
▴ 20
6
votes
7
replies
3.8k
views
GOexpress: use DESeq2 data object as input
GOexpress
deseq2
expressionset
8.6 years ago
martin.hoelzer
▴ 20
3
votes
6
replies
4.5k
views
Analyzing data without replicates using DiffBind
diffbind
bioconductor
differential binding analysis
without replicate
chipseq
6.5 years ago
Hesh
▴ 10
0
votes
9
replies
2.2k
views
DESEQ2 genes with large count variation do not show as differentially expressed
deseq2
8.7 years ago • updated 8.5 years ago
sharvari gujja
▴ 40
0
votes
9
replies
1.8k
views
problem with function rma
Normalization
rat2302
cdf
genefilter
affy
simpleaffy
affyQCReport
affyio
Normalization
updated 17.0 years ago by
Seth Falcon
★ 7.4k • written 17.0 years ago by
julin@aecom.yu.edu
▴ 80
0
votes
10
replies
2.4k
views
assignChromosomeRegion in 2.6.0 ChIPpeakAnno
Microarray
Annotation
GO
Network
Regression
Survival
Infrastructure
Escherichia coli
ROC
11.2 years ago
Julie Zhu
★ 4.3k
5
votes
20
replies
3.1k
views
matching of AAStringSet vs. another AAStringSet
biostrings
AAStringset
7.5 years ago • updated 7.4 years ago
tobias.kockmann
▴ 20
0
votes
8
replies
1.5k
views
Rdbi.PgSQL
19.2 years ago
hrishikesh deshmukh
▴ 420
5
votes
14
replies
15k
views
How to load GEO series matrix file in R Bioconductor
geoquery
updated 8.9 years ago by
Sean Davis
21k • written 8.9 years ago by
ayanava18
▴ 10
0
votes
10
replies
2.9k
views
gene set enrichment
Annotation
Organism
Annotation
Organism
updated 2.2 years ago by
Gordon Smyth
50k • written 11.5 years ago by
Alpesh Querer
▴ 220
3
votes
13
replies
4.5k
views
RPKM and FPKM
rnaseq
8.8 years ago
Asma rabe
▴ 290
0
votes
8
replies
1.6k
views
oligo on R 2.4.1?
GO
Survival
annotate
genefilter
affy
affydata
matchprobes
affyQCReport
affyio
oligo
GO
updated 17.3 years ago by
Seth Falcon
★ 7.4k • written 17.3 years ago by
Jenny Drnevich
★ 2.2k
0
votes
6
replies
1.4k
views
AnnBuilder and Diverse Mappings
Annotation
GO
AnnBuilder
Annotation
GO
AnnBuilder
updated 17.3 years ago by
Nianhua Li
▴ 870 • written 17.3 years ago by
Johannes Graumann
▴ 130
0
votes
9
replies
2.4k
views
backgroundCorrect offset value
updated 12.7 years ago by
Gordon Smyth
50k • written 12.7 years ago by
Prasad Siddavatam
▴ 150
0
votes
9
replies
2.8k
views
Questions about DiffBind loaded peaks and re-count reads
DiffBind
3.5 years ago • updated 2.3 years ago
Tongjun
• 0
0
votes
6
replies
2.5k
views
how to use negative controls to obtain scale and offset parameters then to normalize the whole protein microarray data by vsn method
vsn
protein microarray
normalization
scale and offset parameters
8.7 years ago
guojiegina
• 0
0
votes
14
replies
3.5k
views
Trimming of partial adaptor sequences
Sequencing
Cancer
Biostrings
Sequencing
Cancer
Biostrings
10.8 years ago
Taylor, Sean D
▴ 250
0
votes
11
replies
1.5k
views
Rgraphviz: adding weight to an edge
updated 18.4 years ago by
Jeff Gentry
★ 3.9k • written 18.4 years ago by
Kaustubh Patil
▴ 110
2
votes
8
replies
5.8k
views
StringTie + Ballgown: handling biological replicates
ballgown
stringtie
updated 7.2 years ago by
linda.boshans
• 0 • written 8.2 years ago by
bhawley1991
▴ 10
0
votes
8
replies
6.4k
views
How to sort a matrix based on its column names and preserving the identical column names
updated 16.8 years ago by
alex lam RI
▴ 310 • written 16.8 years ago by
carol white
▴ 680
21
votes
24
replies
13k
views
Problem with biomart's listMarts function
biomart
bug
updated 8.1 years ago by
Paul Shannon
▴ 470 • written 8.5 years ago by
Johannes Rainer
★ 2.0k
4
votes
17
replies
5.5k
views
Upgrade to 3.1 error
software error
updated 8.9 years ago by
Bogdan
▴ 670 • written 9.0 years ago by
Luobin
▴ 10
0
votes
6
replies
1.6k
views
DiffBind error with dba.count
diffbind
updated 6.1 years ago by
Rory Stark
★ 5.2k • written 6.1 years ago by
hhhcce
• 0
0
votes
7
replies
1.4k
views
getBioC and install.packages2 fail
Proteomics
reposTools
Proteomics
reposTools
updated 19.2 years ago by
Seth Falcon
★ 7.4k • written 19.2 years ago by
Arne.Muller@sanofi-aventis.com
▴ 210
0
votes
10
replies
1.4k
views
[Bioc] RNAseq less sensitive than microarrays? Is it a statistical issue?
Microarray
Coverage
Microarray
Coverage
11.0 years ago
Thomas Girke
★ 1.7k
13
votes
21
replies
6.1k
views
modeling zero-dominated RNA-seq with voom/limma and hurdle models (pscl)
limma
voom
hurdle
single cell
8.7 years ago
osa.zuta
▴ 40
0
votes
9
replies
19k
views
dmrcate(): Error in `$<-.data.frame`(`*tmp*`, "sig", value = logical(0)) : replacement has 0 rows, data has 1963
dmrcate
updated 7.4 years ago by
Tim Peters
▴ 180 • written 7.6 years ago by
ew17
• 0
2
votes
7
replies
3.9k
views
edgeR design matrix, one group vs average of other groups
edgeR
edgeR
updated 10.2 years ago by
Gordon Smyth
50k • written 10.2 years ago by
Georg Otto
▴ 120
6
votes
8
replies
2.5k
views
Interaction with DESeq2 via DiffBind
diffbind
deseq2
interactions
updated 3.4 years ago by
pierre.marin
• 0 • written 6.6 years ago by
rbronste
▴ 60
1
vote
10
replies
2.2k
views
FourC object from scratch
hi-c
HiTC
fourcseq
8.6 years ago • updated 8.5 years ago
Nicolas Servant
▴ 260
0
votes
19
replies
2.2k
views
Help with using CRISPRseeker
CRISPR
updated 4.7 years ago by
Julie Zhu
★ 4.3k • written 4.8 years ago by
sharvari gujja
▴ 40
3
votes
9
replies
2.9k
views
ChIPQC and broadPeak input
chipseq
chipqc
chip-seq
8.7 years ago
lindahove
▴ 10
0
votes
10
replies
2.2k
views
Error when using readIDAT() from illuminaio
illuminaio
idat
9.3 years ago • updated 9.2 years ago
lacion
• 0
0
votes
9
replies
1.7k
views
finding and averaging replicate gene records
Microarray
Microarray
19.2 years ago
zhihua li
▴ 120
0
votes
12
replies
2.1k
views
MacOS Package installation problems
BiocInstaller
BiocInstaller
updated 12.0 years ago by
Chinedu Orekie
▴ 10 • written 12.0 years ago by
Michael Salbaum
▴ 80
1
vote
8
replies
1.8k
views
A very large number of diffential genes
deseq2
normalization
8.6 years ago
GFM
▴ 20
1
vote
17
replies
5.6k
views
Filtering out tags with low counts in DESeq and EgdeR?
Normalization
edgeR
DESeq
Normalization
edgeR
DESeq
13.0 years ago
Xiaohui Wu
▴ 280
0
votes
9
replies
1.1k
views
affycoretools
17.4 years ago
Weiyin Zhou
▴ 220
1
vote
8
replies
3.7k
views
normalizing all affymetrix array type with affy package impossible with R 3.x ?
affy normalization affymetrix limma
Readaffy
8.6 years ago
florent.dumont
• 0
1
vote
11
replies
2.0k
views
Does BSgenome.Dmelanogaster.UCSC.dm2 maintain non-coding RNAs?
dm2
bsgenome
noncoding RNA
updated 9.1 years ago by
Hervé Pagès
16k • written 9.1 years ago by
Patrick Schorderet
▴ 20
13
votes
20
replies
14k
views
Can I feed TCGA normalized count data to EdgeR for differential gene expression analysis
EdgeR
TCGA
normalized count
updated 9.2 years ago by
alakatos
▴ 130 • written 9.2 years ago by
ycding
▴ 10
0
votes
6
replies
3.6k
views
batch effect confounded with condition
GO
limma
GO
limma
12.2 years ago
Tefina Paloma
▴ 220
45,685 results • Page
3 of 914
Recent ...
Replies
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Thank you so much!
Answer: recount3 problem downloading data from source sra
by
Leonardo Collado Torres
★ 1.0k
Hi, I wasn't able to reproduce the issue on both bioc 3.19 (current release version) and 3.18 (closer to your session info). My guess is…
Answer: Running ENmix with mouse methylation manifest: readidat error - Error in readman
by
minardsmitha
▴ 10
Well it turns out there is a typo in the manifest file name. This particular issue is resolved by correcting the typo. A new error now …
Answer: Documenting resources in an `ExperimentHub` package?
by
James W. MacDonald
66k
The easiest way to do that IMO is to use emacs/ESS (or I believe there is some newfangled thing called RStudio? Not personally familiar, bu…
Comment: ChAMP installation issue
by
shepherl
3.9k
We are still waiting for the goseq to respond to our requests but will take action next week if it is not resolved. ChAMP is currently una…
Votes
Answer: Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
Comment: Ensembl plants at annotationHub?
how to control age and gender effect in expression data using DESeq2
Answer: Error retrieving ensembl gene id using biomaRt...
Comment: LRT, more than two conditions and pairwise comparisons
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