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Cancer
•
reset
0
votes
13
replies
1.8k
views
Is a number within a set of ranges?
Cancer
Cancer
16.5 years ago
Daniel Brewer
★ 1.9k
0
votes
9
replies
1.8k
views
Re: Manova nuances
Microarray
Cancer
Microarray
Cancer
20.5 years ago
Baker, Stephen
▴ 160
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
8
replies
2.0k
views
AnnBuilder and Kegg
Pathways
GO
Survival
Cancer
Organism
annotate
affydata
vsn
AnnBuilder
globaltest
GO
vsn
updated 17.5 years ago by
David Lapointe
▴ 190 • written 17.5 years ago by
John Zhang
★ 2.9k
0
votes
13
replies
2.1k
views
statistical test for time course data
Cancer
limma
edgeR
Cancer
limma
edgeR
updated 11.2 years ago by
Gordon Smyth
50k • written 11.3 years ago by
chris Jhon
▴ 260
0
votes
18
replies
1.8k
views
normalization and analysis of connected designs
Normalization
Cancer
Normalization
Cancer
updated 20.8 years ago by
Xavier Solé
▴ 20 • written 20.9 years ago by
Ramon Diaz
★ 1.1k
0
votes
6
replies
1.4k
views
hyperGTest
GO
Cancer
GOstats
Category
GO
Cancer
GOstats
Category
updated 17.0 years ago by
Naomi Altman
★ 6.0k • written 17.0 years ago by
Seth Falcon
★ 7.4k
0
votes
9
replies
1.4k
views
matrix row/column displayed as a list
Cancer
Cancer
updated 17.1 years ago by
Seth Falcon
★ 7.4k • written 17.1 years ago by
Daniel Brewer
★ 1.9k
0
votes
8
replies
1.6k
views
Large # of significant genes with SAM
Cancer
affy
Cancer
affy
updated 19.0 years ago by
Charles Berry
▴ 290 • written 19.0 years ago by
Vincent Detours
▴ 80
0
votes
7
replies
1.4k
views
Gene Ontology relationships
Cancer
GOstats
Cancer
GOstats
updated 16.9 years ago by
Dick Beyer
★ 1.4k • written 16.9 years ago by
Seth Falcon
★ 7.4k
1
vote
5
replies
2.1k
views
Finding differentially expressed genes using Ebayes
Cancer
Cancer
updated 15.0 years ago by
James W. MacDonald
65k • written 15.0 years ago by
John Herbert
▴ 90
0
votes
7
replies
3.2k
views
Visualise KEGG pathway and highlight genes
Cancer
KEGGgraph
Cancer
KEGGgraph
updated 15.1 years ago by
Paolo Sonego
▴ 140 • written 15.1 years ago by
Daniel Brewer
★ 1.9k
0
votes
10
replies
1.9k
views
comparing GO lists
Annotation
GO
Cancer
graph
GOstats
Annotation
GO
Cancer
graph
GOstats
updated 16.8 years ago by
Ana Conesa
▴ 130 • written 16.8 years ago by
rgentleman
★ 5.5k
0
votes
9
replies
1.6k
views
RE: Advice on print-tip normalization
Cancer
probe
marray
oligo
Cancer
probe
marray
oligo
updated 19.6 years ago by
Gene Cutler
▴ 50 • written 19.6 years ago by
Mark Reimers
▴ 70
0
votes
9
replies
1.7k
views
gains and losses via mode shifting
Cancer
CGH
Cancer
CGH
15.8 years ago
Oscar Rueda
▴ 60
0
votes
7
replies
1.5k
views
I have trouble running the AnnBuilder Vignette
Cancer
Organism
AnnBuilder
Cancer
Organism
AnnBuilder
updated 19.5 years ago by
James W. MacDonald
65k • written 19.5 years ago by
Richard Friedman
★ 2.0k
0
votes
10
replies
1.7k
views
exonmap RMA function
Microarray
Cancer
affyPLM
exonmap
Microarray
Cancer
affyPLM
exonmap
updated 16.3 years ago by
Yuan Jian
▴ 250 • written 16.3 years ago by
Martin Morgan
25k
0
votes
5
replies
1.6k
views
biomaRt/RMySQL installation help
Cancer
biomaRt
Cancer
biomaRt
updated 18.7 years ago by
Seth Falcon
★ 7.4k • written 18.7 years ago by
Jane Fridlyand
▴ 90
0
votes
10
replies
1.8k
views
AgiMicroRNA and Extra columns in Agilent Mouse miRNA Microarray Release 12.0 G4471A-021828.
miRNA
Microarray
Cancer
microRNA
miRNA
Microarray
Cancer
microRNA
13.9 years ago
Neel Aluru
▴ 460
0
votes
10
replies
1.9k
views
Some Genefilter questions
Normalization
Survival
Cancer
cdf
genefilter
geneplotter
affy
affydata
widgetTools
gcrma
updated 17.4 years ago by
Amy Mikhail
▴ 460 • written 17.4 years ago by
David K Pritchard
▴ 70
0
votes
5
replies
1.3k
views
A question about the function readGAlignmentPairs in GenomicRnages package
Cancer
Cancer
10.1 years ago
Hervé Pagès
16k
0
votes
5
replies
1.2k
views
homology package question
Microarray
Cancer
Microarray
Cancer
updated 17.1 years ago by
John Zhang
★ 2.9k • written 17.1 years ago by
James W. MacDonald
65k
0
votes
5
replies
3.2k
views
overlap regions between two GRanges (or GRangesList)
Cancer
Cancer
updated 10.1 years ago by
Shanrong Zhao
▴ 20 • written 10.1 years ago by
Hervé Pagès
16k
0
votes
5
replies
2.1k
views
DESeq and paired samples - pairing vs pooling
Cancer
DESeq
Cancer
DESeq
updated 13.0 years ago by
Gordon Smyth
50k • written 13.0 years ago by
Timothy Hughes
▴ 20
0
votes
14
replies
2.7k
views
RBGL 1.8.1 installation error on linux
Cancer
graph
RBGL
Cancer
graph
RBGL
updated 17.9 years ago by
Li.Long@isb-sib.ch
▴ 510 • written 18.0 years ago by
Johannes Rainer
▴ 300
0
votes
5
replies
1.5k
views
Best options for cross validation machine learning
Microarray
Clustering
Cancer
Microarray
Clustering
Cancer
updated 14.3 years ago by
Joern Toedling
▴ 450 • written 14.3 years ago by
Daniel Brewer
★ 1.9k
0
votes
5
replies
1.6k
views
Software to find the area of a shape in an image
Cancer
Cancer
updated 14.8 years ago by
Jordi Altirriba Gutiérrez
▴ 350 • written 14.8 years ago by
Daniel Brewer
★ 1.9k
0
votes
5
replies
1.5k
views
Errors using biocLite on Apple OS X
GUI
Cancer
Breast
Biobase
GUI
Cancer
Breast
Biobase
17.8 years ago
Steven McKinney
▴ 310
0
votes
8
replies
1.6k
views
ChIPpeakAnno Strandedness and distance calculation
Annotation
Cancer
ChIPpeakAnno
Annotation
Cancer
ChIPpeakAnno
updated 14.0 years ago by
Dario Strbenac
★ 1.5k • written 14.0 years ago by
Julie Zhu
★ 4.3k
0
votes
4
replies
1.3k
views
How do you keep track of your analyses
Cancer
Cancer
updated 15.6 years ago by
Bio Sam
▴ 60 • written 15.6 years ago by
Daniel Brewer
★ 1.9k
0
votes
6
replies
1.7k
views
RE: RMA normalization
Normalization
Cancer
Normalization
Cancer
updated 19.6 years ago by
Wolfgang Huber
★ 13k • written 19.6 years ago by
Mark Reimers
▴ 70
0
votes
3
replies
1.6k
views
PCA plots
Cancer
Cancer
updated 21.3 years ago by
rgentleman
★ 5.5k • written 21.3 years ago by
Michael Benjamin
▴ 120
0
votes
4
replies
2.1k
views
biomaRt get exon intron structure of a transcrit
Cancer
biomaRt
Cancer
biomaRt
15.5 years ago
Shi, Tao
▴ 720
0
votes
3
replies
1.6k
views
RE: quantile normalization
Normalization
Cancer
PROcess
Normalization
Cancer
PROcess
updated 19.7 years ago by
H. Han
▴ 30 • written 19.7 years ago by
Mark Reimers
▴ 70
0
votes
4
replies
1.3k
views
GOstats: another problem
GO
Cancer
GO
Cancer
19.8 years ago
John Zhang
★ 2.9k
0
votes
4
replies
1.3k
views
Removing libraries or using a particular function
Cancer
DNAcopy
Cancer
DNAcopy
updated 16.8 years ago by
Seth Falcon
★ 7.4k • written 16.8 years ago by
Daniel Brewer
★ 1.9k
0
votes
6
replies
1.3k
views
install Monograph problem
Cancer
widgetTools
Cancer
widgetTools
17.0 years ago
Seth Falcon
★ 7.4k
0
votes
3
replies
1.5k
views
AnnBuilder/ABPkgBuilder: lots of Errors
Annotation
GO
Cancer
Organism
Biobase
annotate
AnnBuilder
PROcess
bridge
Annotation
GO
updated 19.7 years ago by
John Zhang
★ 2.9k • written 19.7 years ago by
Floor Stam
▴ 90
0
votes
4
replies
1.3k
views
GOstats locked database
GO
Cancer
GOstats
GO
Cancer
GOstats
16.3 years ago
Janet Young
▴ 740
0
votes
3
replies
2.1k
views
gene expression data followup
Survival
Cancer
Survival
Cancer
updated 15.5 years ago by
James W. MacDonald
65k • written 15.5 years ago by
Adrian Johnson
▴ 330
0
votes
3
replies
2.4k
views
Reading in data with HTqPCR
Cancer
cycle
Cancer
cycle
updated 13.9 years ago by
deepak roshan
▴ 40 • written 13.9 years ago by
Heidi Dvinge
★ 2.0k
0
votes
3
replies
1.8k
views
"scale to fit" plot for A4 pdf
Cancer
a4
Cancer
a4
updated 17.1 years ago by
James W. MacDonald
65k • written 17.1 years ago by
Daniel Brewer
★ 1.9k
0
votes
6
replies
1.2k
views
matrix row/column displayed as a list
Cancer
Cancer
updated 17.1 years ago by
Seth Falcon
★ 7.4k • written 17.1 years ago by
Daniel Brewer
★ 1.9k
0
votes
4
replies
10k
views
Correlation matrix and pca on matrix with NA values
Cancer
Cancer
updated 17.1 years ago by
Aedin Culhane
▴ 510 • written 17.1 years ago by
Daniel Brewer
★ 1.9k
0
votes
5
replies
1.6k
views
Importing CDF file for custom array using makecdfenv
Microarray
GO
Survival
Cancer
cdf
Biobase
annotate
genefilter
affy
graph
makecdfenv
GO
updated 17.5 years ago by
Sung-Chur Sim
▴ 20 • written 17.5 years ago by
Jenny Drnevich
★ 2.2k
0
votes
4
replies
1.4k
views
Re: technical replicates (again!): a summary
Microarray
GO
Cancer
vsn
Microarray
GO
Cancer
vsn
updated 20.1 years ago by
Ramon Diaz
★ 1.1k • written 20.1 years ago by
Gordon Smyth
50k
0
votes
5
replies
1.8k
views
RMA and justRMA error
Cancer
cdf
Biobase
affy
gcrma
affyio
Cancer
cdf
Biobase
affy
gcrma
affyio
17.7 years ago
Aedin Culhane
▴ 510
0
votes
7
replies
1.4k
views
M vs A plot
Microarray
Normalization
Regression
Cancer
marray
Microarray
Normalization
Regression
updated 20.2 years ago by
Naomi Altman
★ 6.0k • written 20.2 years ago by
Richard Friedman
★ 2.0k
0
votes
5
replies
1.5k
views
Display of histogram of RMA-processed data
Cancer
Cancer
20.0 years ago
Richard Friedman
★ 2.0k
0
votes
8
replies
1.9k
views
raw probe set expression data and masking questions
Normalization
Cancer
probe
affy
PROcess
Normalization
Cancer
probe
affy
PROcess
updated 7.1 years ago by
jacorvar
▴ 40 • written 17.7 years ago by
Schwartz, Donald
▴ 20
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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