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Views
Votes
0
votes
9
replies
1.0k
views
affycoretools
17.4 years ago
Weiyin Zhou
▴ 220
2
votes
12
replies
2.3k
views
Synapter - makeMaster() and synergise() functions warnings/fails
software error
warnings
synapter
9.4 years ago
sogueta
• 0
0
votes
9
replies
1.8k
views
problem with function rma
Normalization
rat2302
cdf
genefilter
affy
simpleaffy
affyQCReport
affyio
Normalization
updated 16.9 years ago by
Seth Falcon
★ 7.4k • written 16.9 years ago by
julin@aecom.yu.edu
▴ 80
0
votes
12
replies
3.5k
views
Understanding limma, fdr and topTable
Microarray
GO
limma
Microarray
GO
limma
updated 15.8 years ago by
Robson, Samuel
▴ 10 • written 15.8 years ago by
Louisa A Rispoli/AS/EXP/UTIA
▴ 160
0
votes
6
replies
1.5k
views
DiffBind error with dba.count
diffbind
updated 6.0 years ago by
Rory Stark
★ 5.2k • written 6.1 years ago by
hhhcce
• 0
1
vote
6
replies
2.1k
views
SGSeq error on analyzeFeatures
SGSeq
analyzeFeatures
Splicing
9.4 years ago
Paolo Guarnieri
▴ 20
0
votes
9
replies
1.7k
views
finding and averaging replicate gene records
Microarray
Microarray
19.2 years ago
zhihua li
▴ 120
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
1
vote
9
replies
3.7k
views
DESeq: Error in model.matrix.formula(design(object), data = colData(object)) : data must be a data.frame
deseq2
updated 3.8 years ago by
thind.amarinder
▴ 10 • written 8.1 years ago by
mdelrgg
▴ 10
0
votes
10
replies
4.1k
views
edgeR outlier question
RNASeq
edgeR
RNASeq
edgeR
updated 12.0 years ago by
Gordon Smyth
50k • written 12.0 years ago by
Simon Melov
▴ 340
2
votes
7
replies
3.8k
views
edgeR design matrix, one group vs average of other groups
edgeR
edgeR
updated 10.1 years ago by
Gordon Smyth
50k • written 10.2 years ago by
Georg Otto
▴ 120
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
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 6.5 years ago by
rbronste
▴ 60
1
vote
10
replies
3.0k
views
ShortRead with large fastq files
shortread
8.9 years ago
danova_fr
▴ 20
0
votes
10
replies
1.3k
views
[Bioc] RNAseq less sensitive than microarrays? Is it a statistical issue?
Microarray
Coverage
Microarray
Coverage
11.0 years ago
Thomas Girke
★ 1.7k
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 • updated 11.1 years ago
Julie Zhu
★ 4.3k
4
votes
17
replies
5.5k
views
Upgrade to 3.1 error
software error
updated 8.8 years ago by
Bogdan
▴ 670 • written 9.0 years ago by
Luobin
▴ 10
13
votes
21
replies
6.0k
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
1
vote
10
replies
2.2k
views
FourC object from scratch
hi-c
HiTC
fourcseq
8.6 years ago • updated 8.4 years ago
Nicolas Servant
▴ 260
2
votes
8
replies
2.6k
views
read.FCS fails on BioRad FCS files
flowCore
8.6 years ago
Robert Baer
▴ 70
1
vote
8
replies
1.8k
views
A very large number of diffential genes
deseq2
normalization
8.6 years ago • updated 8.5 years ago
GFM
▴ 20
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 17.2 years ago by
Seth Falcon
★ 7.4k • written 17.2 years ago by
Jenny Drnevich
★ 2.2k
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 9.1 years ago by
pbhamidipati
• 0
0
votes
9
replies
2.7k
views
Questions about DiffBind loaded peaks and re-count reads
DiffBind
3.4 years ago • updated 2.2 years ago
Tongjun
• 0
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 7.3 years ago by
Tim Peters
▴ 180 • written 7.5 years ago by
ew17
• 0
0
votes
10
replies
2.2k
views
Error when using readIDAT() from illuminaio
illuminaio
idat
9.2 years ago
lacion
• 0
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
8
votes
16
replies
3.2k
views
matrix transposing in R
affy mas5
updated 8.8 years ago by
arfranco
▴ 130 • written 8.8 years ago by
Angel
▴ 40
0
votes
10
replies
2.8k
views
gene set enrichment
Annotation
Organism
Annotation
Organism
updated 2.1 years ago by
Gordon Smyth
50k • written 11.4 years ago by
Alpesh Querer
▴ 220
1
vote
11
replies
1.9k
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
6
votes
7
replies
3.8k
views
GOexpress: use DESeq2 data object as input
GOexpress
deseq2
expressionset
8.6 years ago
martin.hoelzer
▴ 20
0
votes
6
replies
1.4k
views
AnnBuilder and Diverse Mappings
Annotation
GO
AnnBuilder
Annotation
GO
AnnBuilder
updated 17.2 years ago by
Nianhua Li
▴ 870 • written 17.2 years ago by
Johannes Graumann
▴ 130
0
votes
7
replies
1.6k
views
bioconductor
Microarray
affy
Microarray
affy
updated 20.5 years ago by
Yuk Fai Leung
▴ 100 • written 20.5 years ago by
Roger Vallejo
▴ 120
0
votes
8
replies
1.6k
views
GOstats error messages
Annotation
rat2302
Annotation
rat2302
18.6 years ago
Kimpel, Mark W
▴ 890
0
votes
19
replies
2.2k
views
Help with using CRISPRseeker
CRISPR
updated 4.7 years ago by
Julie Zhu
★ 4.3k • written 4.7 years ago by
sharvari gujja
▴ 40
0
votes
10
replies
2.6k
views
Very low P-values in limma
miRNA
limma
microRNA
miRNA
limma
microRNA
updated 14.5 years ago by
Olga Vitek
▴ 40 • written 14.5 years ago by
Paul Geeleher
★ 1.3k
0
votes
7
replies
1.2k
views
Installing bioconductor under MacOsx
reposTools
reposTools
updated 21.0 years ago by
Byron Ellis
▴ 280 • written 21.0 years ago by
Martino Barenco
▴ 110
0
votes
12
replies
2.1k
views
MacOS Package installation problems
BiocInstaller
BiocInstaller
updated 11.9 years ago by
Chinedu Orekie
▴ 10 • written 11.9 years ago by
Michael Salbaum
▴ 80
2
votes
8
replies
5.7k
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
9
replies
2.2k
views
DESEQ2 genes with large count variation do not show as differentially expressed
deseq2
8.6 years ago • updated 8.5 years ago
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
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
2
votes
20
replies
10k
views
problem loading lumi package, Error : object ‘sqliteQuickSQL’ is not exported by 'namespace:RSQLite'
lumi
updated 9.0 years ago by
laseaman
• 0 • written 9.5 years ago by
lucashusquin
▴ 10
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
3
votes
6
replies
4.4k
views
Analyzing data without replicates using DiffBind
diffbind
bioconductor
differential binding analysis
without replicate
chipseq
6.5 years ago
Hesh
▴ 10
3
votes
13
replies
4.5k
views
RPKM and FPKM
rnaseq
8.8 years ago
Asma rabe
▴ 290
16
votes
9
replies
6.5k
views
Diffbind: edgeR or DESeq2 ?
diffbind
medip-seq
edger
deseq2
updated 6.5 years ago by
Rory Stark
★ 5.2k • written 8.1 years ago by
florian.noack
▴ 60
0
votes
7
replies
1.4k
views
getBioC and install.packages2 fail
Proteomics
reposTools
Proteomics
reposTools
updated 19.1 years ago by
Seth Falcon
★ 7.4k • written 19.1 years ago by
Arne.Muller@sanofi-aventis.com
▴ 210
5
votes
20
replies
3.1k
views
matching of AAStringSet vs. another AAStringSet
biostrings
AAStringset
7.4 years ago
tobias.kockmann
▴ 20
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 • updated 8.6 years ago
guojiegina
• 0
45,620 results • Page
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Answer: Method to find pathways different between 2 groups
by
Gordon Smyth
50k
> When I search camera limma on pubmed, I found 2 papers I am unclear what point you are trying to make. limma's camera method has been fo…
Comment: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
limma most certainly is available. It installs in R 4.4.0 and Bioc 3.19 for all platforms without any issues. It has not had any period of …
Comment: package goseq seems to be not available on the latest version of R
by
Patrycja
▴ 20
limma package also isn't available.Is there any information when these packages will be available?
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
41k
Check the number of bootstrapped data per chromosome compared to the original, and then you can also look at its distribution. For this it'…
Comment: DNAString: Standard checksum function?
by
Henrik Bengtsson
★ 2.4k
For completeness: SEGUID v2 (https://www.seguid.org/), implemented in CRAN package **[seguid](https://cran.r-project.org/package=seguid)*…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Handling multiple differential expression comparisons
Answer: fgsea significant result
Answer: fgsea significant result
package goseq seems to be not available on the latest version of R
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