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Views
Votes
0
votes
9
replies
1.0k
views
affycoretools
17.4 years ago
Weiyin Zhou
▴ 220
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
2
votes
12
replies
2.3k
views
Synapter - makeMaster() and synergise() functions warnings/fails
software error
warnings
synapter
9.5 years ago • updated 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 17.0 years ago by
Seth Falcon
★ 7.4k • written 17.0 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 15.9 years ago by
Louisa A Rispoli/AS/EXP/UTIA
▴ 160
1
vote
6
replies
2.2k
views
SGSeq error on analyzeFeatures
SGSeq
analyzeFeatures
Splicing
9.4 years ago
Paolo Guarnieri
▴ 20
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
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
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
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
1.5k
views
Rdbi.PgSQL
19.2 years ago • updated 19.1 years ago
hrishikesh deshmukh
▴ 420
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
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
1
vote
8
replies
1.8k
views
A very large number of diffential genes
deseq2
normalization
8.6 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 17.3 years ago by
Seth Falcon
★ 7.4k • written 17.3 years ago by
Jenny Drnevich
★ 2.2k
3
votes
13
replies
4.5k
views
RPKM and FPKM
rnaseq
8.8 years ago
Asma rabe
▴ 290
21
votes
24
replies
13k
views
Problem with biomart's listMarts function
biomart
bug
updated 8.0 years ago by
Paul Shannon
▴ 470 • written 8.5 years ago by
Johannes Rainer
★ 2.0k
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
0
votes
6
replies
1.5k
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
2
votes
8
replies
2.6k
views
read.FCS fails on BioRad FCS files
flowCore
8.6 years ago
Robert Baer
▴ 70
0
votes
9
replies
2.7k
views
Questions about DiffBind loaded peaks and re-count reads
DiffBind
3.5 years ago • updated 2.2 years ago
Tongjun
• 0
8
votes
16
replies
3.2k
views
matrix transposing in R
affy mas5
updated 8.8 years ago by
arfranco
▴ 130 • written 8.9 years ago by
Angel
▴ 40
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
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
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 14.6 years ago by
Paul Geeleher
★ 1.3k
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
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
10
replies
2.2k
views
Error when using readIDAT() from illuminaio
illuminaio
idat
9.2 years ago
lacion
• 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
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
0
votes
6
replies
3.6k
views
batch effect confounded with condition
GO
limma
GO
limma
12.2 years ago
Tefina Paloma
▴ 220
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 7.5 years ago by
ew17
• 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
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
8
replies
1.6k
views
GOstats error messages
Annotation
rat2302
Annotation
rat2302
18.7 years ago • updated 18.6 years ago
Kimpel, Mark W
▴ 890
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
2.4k
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
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
1.8k
views
Re: Manova nuances
Microarray
Cancer
Microarray
Cancer
20.5 years ago
Baker, Stephen
▴ 160
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
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
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
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
2
votes
7
replies
3.8k
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
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 9.1 years ago by
alakatos
▴ 130 • written 9.1 years ago by
ycding
▴ 10
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
5
votes
14
replies
14k
views
How to load GEO series matrix file in R Bioconductor
geoquery
updated 8.8 years ago by
Sean Davis
21k • written 8.8 years ago by
ayanava18
▴ 10
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
45,636 results • Page
3 of 913
Recent ...
Replies
Comment: deseq2 results
by
swbarnes2
★ 1.4k
Ask the people who made the libraires if there was anything unusual in the QC of the outlier sample. Try to figure out what biologically …
Comment: Can't post a question containing code?
by
NATASHA
• 0
did you find a solution? I´m having the same problem
Comment: error
by
NATASHA
• 0
Please ignore, i didnt copy all the scrip
Comment: Extremely small p-values using Limma for proteomic data
by
James W. MacDonald
65k
If you ever find yourself using the `@` function, you should reconsider what you are doing. There are vanishingly small instances when an e…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
42k
Here is some example code <https://gist.github.com/mikelove/cbbc84634b6854c865cb5eb08ad9b245>
Votes
A: AIC-like measure for DESeq2
Comment: Extremely small p-values using Limma for proteomic data
Comment: Log-cpm values from limma
Comment: Log-cpm values from limma
Comment: deseq2 results
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