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glad
•
reset
0
votes
0
replies
1.2k
views
DiffBind (Please add me to the Dropbox containing the vignette data)
GLAD
edgeR
DiffBind
DESeq2
GLAD
edgeR
DiffBind
DESeq2
10.1 years ago
Rory Stark
★ 5.2k
0
votes
0
replies
916
views
Limma design : What is the
GLAD
GLAD
10.2 years ago
Santy Marques-Ladeira
▴ 20
0
votes
3
replies
1.3k
views
GLAD crashes when built with gcc-4.8
GLAD
GLAD
updated 10.4 years ago by
Martin Morgan
25k • written 10.4 years ago by
Ramon Diaz-Uriarte
▴ 70
0
votes
0
replies
768
views
arrayQualityMetrics does not produce interactive plots
GLAD
GLAD
10.4 years ago
Wolfgang Huber
★ 13k
0
votes
0
replies
2.2k
views
makeTranscriptDbFromGFF fails on NCBI Bacteria
Alignment
Annotation
Normalization
GO
Preprocessing
Clustering
Cancer
Organism
probe
GLAD
10.7 years ago
Sarah Pohl
▴ 30
0
votes
3
replies
2.0k
views
Diffbind: Binding Affinity Heatmap
Sequencing
GO
Clustering
GLAD
edgeR
DESeq
DiffBind
Sequencing
GO
Clustering
GLAD
edgeR
10.7 years ago
Rory Stark
★ 5.2k
0
votes
1
reply
1.0k
views
beadarray library: perBeadFile
GLAD
beadarray
GLAD
beadarray
updated 10.7 years ago by
Mike Smith
★ 6.5k • written 10.8 years ago by
Nogales Vilardell
▴ 10
0
votes
1
reply
1.7k
views
Issue of installing the GLAD package
GLAD
GLAD
updated 10.9 years ago by
Laurent Gatto
1.6k • written 10.9 years ago by
Guest User
★ 13k
1
vote
1
reply
2.0k
views
multiple threads on QuasR
Alignment
GLAD
QuasR
Alignment
GLAD
QuasR
11.1 years ago • updated 11.0 years ago
Michael Stadler
▴ 350
0
votes
0
replies
924
views
rhdf5 and factors
GO
GLAD
GO
GLAD
11.3 years ago
Stephen Eglen
▴ 10
0
votes
3
replies
1.6k
views
Merging various panel for flow cytometry
GLAD
flowCore
flowViz
GLAD
flowCore
flowViz
updated 11.4 years ago by
Jiang, Mike
★ 1.3k • written 11.4 years ago by
TEXTORIS Julien
▴ 160
0
votes
0
replies
859
views
question on easyRNASeq developer version
GLAD
easyRNASeq
GLAD
easyRNASeq
11.6 years ago
delhomme@embl.de
★ 1.2k
0
votes
2
replies
1.5k
views
DESeq - Estimating Dispersion with Technical Replicates
GLAD
DESeq
GLAD
DESeq
updated 11.6 years ago by
Wolfgang Huber
★ 13k • written 11.6 years ago by
Andres Eduardo Rodriguez Cubillos
▴ 20
0
votes
0
replies
1.1k
views
question regarding ChIPPeakAnno use
Annotation
annotate
GLAD
ChIPpeakAnno
Annotation
annotate
GLAD
ChIPpeakAnno
11.6 years ago
Julie Zhu
★ 4.3k
0
votes
0
replies
1.1k
views
HTqPCR problems
Microarray
qPCR
GO
Preprocessing
GLAD
HTqPCR
Microarray
qPCR
GO
Preprocessing
GLAD
11.7 years ago
cfischer
▴ 10
0
votes
0
replies
818
views
(no subject)
Clustering
probe
limma
GLAD
Clustering
probe
limma
GLAD
11.7 years ago
Gordon Smyth
50k
0
votes
4
replies
1.4k
views
HTqPCR problems
qPCR
GO
Preprocessing
GLAD
HTqPCR
qPCR
GO
Preprocessing
GLAD
HTqPCR
updated 11.8 years ago by
Simon Melov
▴ 340 • written 11.8 years ago by
Heidi Dvinge
★ 2.0k
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
13
replies
1.9k
views
PWMscoreStartingAt and ambiguous subject seqs
Cancer
Biostrings
GLAD
Cancer
Biostrings
GLAD
updated 12.0 years ago by
Hervé Pagès
16k • written 12.0 years ago by
Janet Young
▴ 740
0
votes
0
replies
2.6k
views
gene set enrichment analysis of RNA-Seq data
Microarray
limma
GLAD
edgeR
goseq
Microarray
limma
GLAD
edgeR
goseq
12.0 years ago
Paolo Guarnieri
▴ 20
0
votes
0
replies
1.1k
views
Fwd: RCytoscape couldn't connect to host
GO
GLAD
RCytoscape
GO
GLAD
RCytoscape
12.0 years ago
Paul Shannon
▴ 750
0
votes
0
replies
1.2k
views
[Rocky] - R code for PGSEA package to identify differentially expressed genes
GO
affy
limma
GLAD
PGSEA
GSEABase
GO
affy
limma
GLAD
PGSEA
GSEABase
12.3 years ago
Valerie Obenchain
★ 6.8k
0
votes
1
reply
1.6k
views
Rgraphviz installing problem
Rgraphviz
GLAD
Rgraphviz
GLAD
updated 12.3 years ago by
Martin Morgan
25k • written 12.3 years ago by
Alexandra Federer
▴ 10
0
votes
1
reply
868
views
[Rocky] - LIMMA to identify deferentially expressed genes
affy
limma
GLAD
affy
limma
GLAD
updated 12.3 years ago by
Sean Davis
21k • written 12.3 years ago by
하오잠 로
▴ 30
0
votes
0
replies
946
views
edgeR - R script - results compared to DESeq
GLAD
edgeR
DESeq
GLAD
edgeR
DESeq
12.4 years ago
Gordon Smyth
50k
0
votes
2
replies
1.4k
views
error in loading GLAD package
GLAD
GLAD
updated 12.5 years ago by
Martin Morgan
25k • written 12.5 years ago by
Qian Liu
▴ 110
0
votes
1
reply
1.6k
views
[Bioc-sig-seq] as.data.frame on GRanges object with DNAStringSet in values
Cancer
Biostrings
GLAD
Cancer
Biostrings
GLAD
updated 12.6 years ago by
Michael Lawrence
★ 11k • written 12.6 years ago by
Hervé Pagès
16k
0
votes
0
replies
1.5k
views
I: R: R: R: Probe-level analysis of exon arrays using xps
Annotation
Normalization
Preprocessing
Breast
Prostate
probe
GLAD
Category
xps
Annotation
12.6 years ago
Lavorgna Giovanni
▴ 80
0
votes
2
replies
842
views
Help with the weaver example from limma package
Annotation
GLAD
Annotation
GLAD
updated 12.9 years ago by
Gordon Smyth
50k • written 12.9 years ago by
Marcus Nunes
▴ 20
0
votes
1
reply
879
views
Rgraphviz windows version incompatible with current Graphviz
Rgraphviz
PROcess
GLAD
Rgraphviz
PROcess
GLAD
updated 13.0 years ago by
Martin Morgan
25k • written 13.0 years ago by
Gregory D.Rodd
▴ 10
0
votes
1
reply
1.3k
views
how to do paired t-tests for multiple subgroups [was: warnings or potential problems in limma procedure]
Cancer
limma
GLAD
Category
Cancer
limma
GLAD
Category
updated 13.1 years ago by
Yi, Ming NIH/NCI [C]
▴ 100 • written 13.1 years ago by
Gordon Smyth
50k
0
votes
1
reply
1.3k
views
edgeR glm fit error
GO
GLAD
edgeR
GO
GLAD
edgeR
13.2 years ago
Gordon Smyth
50k
0
votes
1
reply
846
views
Newbie question
GLAD
GLAD
updated 13.3 years ago by
James W. MacDonald
65k • written 13.3 years ago by
quantrum75
▴ 30
0
votes
1
reply
1.4k
views
[Rocky] - Clarification for finding SNPs at 3'UTR, 5'UTR, CDS genomic regions
SNP
Cancer
GLAD
SNP
Cancer
GLAD
updated 13.3 years ago by
Hervé Pagès
16k • written 13.3 years ago by
하오잠 로
▴ 30
0
votes
2
replies
2.2k
views
problem installing 'GLAD' package
cdf
GLAD
cdf
GLAD
13.4 years ago
Shenglin Zheng
▴ 20
0
votes
0
replies
877
views
HTqPCR question
Microarray
limma
GLAD
HTqPCR
Microarray
limma
GLAD
HTqPCR
13.5 years ago
Heidi Dvinge
★ 2.0k
0
votes
0
replies
1.2k
views
error in plotKEGGGraph
Pathways
GLAD
KEGGgraph
Pathways
GLAD
KEGGgraph
13.6 years ago
Robert M. Flight
▴ 280
0
votes
1
reply
1.3k
views
write.XStringView/write.XStringSet highly inefficient (solved)
Cancer
BSgenome
PROcess
GLAD
BSgenome
Cancer
BSgenome
PROcess
GLAD
BSgenome
updated 13.8 years ago by
Steve Lianoglou
★ 13k • written 13.8 years ago by
Michael Dondrup
▴ 550
0
votes
1
reply
1.6k
views
Design matrix for time course analysis with maSigPro
GLAD
maSigPro
GLAD
maSigPro
updated 13.9 years ago by
Wolfgang Huber
★ 13k • written 13.9 years ago by
Matthias Boeck
▴ 10
0
votes
4
replies
1.1k
views
Discrepancy on results from gcrma function and justGCRMA
gcrma
GLAD
gcrma
GLAD
updated 14.3 years ago by
James W. MacDonald
65k • written 14.3 years ago by
Jenny Drnevich
★ 2.0k
0
votes
4
replies
1.5k
views
Positive correlation between dye-swap technical replicates
Normalization
Clustering
probe
limma
GLAD
Normalization
Clustering
probe
limma
GLAD
14.3 years ago
Michał Góralski
▴ 40
0
votes
13
replies
1.7k
views
problem with data processing in R
PROcess
GLAD
PROcess
GLAD
updated 14.4 years ago by
Thomas Girke
★ 1.7k • written 14.4 years ago by
Maxim
▴ 170
0
votes
7
replies
1.4k
views
problem to compute copy number with crlmm
GLAD
crlmm
GLAD
crlmm
updated 14.5 years ago by
Rob Scharpf
▴ 250 • written 14.5 years ago by
Sören Gröttrup
▴ 40
0
votes
0
replies
1.0k
views
general CGH threshold question
aCGH
CGH
aCGH
GLAD
snapCGH
aCGH
CGH
aCGH
GLAD
snapCGH
14.7 years ago
Wolfgang RAFFELSBERGER
▴ 140
0
votes
0
replies
5.1k
views
Reading GFF files into R and GenomeGraphs
Coverage
Annotation
Visualization
convert
GLAD
GenomeGraphs
rtracklayer
IRanges
Coverage
14.7 years ago
Michael Dondrup
▴ 140
0
votes
4
replies
3.1k
views
retrieving mRNA sequences via biomaRt
GLAD
biomaRt
GLAD
biomaRt
updated 14.8 years ago by
Wolfgang Huber
★ 13k • written 14.8 years ago by
Simon
▴ 30
0
votes
1
reply
1.1k
views
Normalized data in expresso and Expression Console differ
Normalization
GLAD
Normalization
GLAD
updated 14.9 years ago by
cstrato
★ 3.9k • written 14.9 years ago by
Oliver Stolpe
▴ 10
0
votes
0
replies
1.1k
views
browseGenome width question (rtracklayer)
Epigenetics
GO
hgu95av2
GLAD
rtracklayer
Epigenetics
GO
hgu95av2
GLAD
rtracklayer
15.3 years ago
Michael Lawrence
▴ 620
0
votes
0
replies
1.7k
views
getSeq human genomic sequences
Annotation
Cancer
BSgenome
PROcess
GLAD
BSgenome
IRanges
Annotation
Cancer
BSgenome
GLAD
15.3 years ago
Hervé Pagès
16k
0
votes
2
replies
1.3k
views
Problem with Annotation of Mouse4302.db in simpleaffy
Annotation
mouse4302
simpleaffy
GLAD
Annotation
mouse4302
simpleaffy
GLAD
updated 15.3 years ago by
James W. MacDonald
65k • written 15.3 years ago by
Marietta Herrmann
▴ 40
50 results • Page
1 of 1
Recent ...
Replies
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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