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Showing :
siggenes
•
reset
2
votes
2
replies
1.4k
views
SAM/siggenes: Differential gene expression analysis
SAM
siggenes
microarray
gene expression
sam
7.3 years ago
Brian Smith
▴ 120
2
votes
4
replies
1.3k
views
Interprentation of appropriate statistical test
samr
SAM
siggenes
bioconductor
differential gene expression
9.3 years ago
svlachavas
▴ 830
1
vote
0
replies
1.8k
views
DE analysis of PCR array [was: dataset dim for siggenes]
qPCR
Normalization
multtest
limma
siggenes
9.6 years ago • updated 7.3 years ago
Gordon Smyth
50k
0
votes
5
replies
1.5k
views
dataset dim for siggenes
qPCR
limma
siggenes
updated 9.7 years ago by
James W. MacDonald
65k • written 9.7 years ago by
Frederico Moraes Ferreira
▴ 100
0
votes
1
reply
1.3k
views
SAM analysis of two color microarray data
Normalization
limma
siggenes
updated 9.7 years ago by
James W. MacDonald
65k • written 9.7 years ago by
Guest User
★ 13k
0
votes
1
reply
1.2k
views
Unexpected results of differential expression analysis
GO
limma
siggenes
GO
limma
siggenes
updated 10.9 years ago by
Wolfgang Huber
★ 13k • written 10.9 years ago by
Guest User
★ 13k
0
votes
3
replies
1.9k
views
runSPIA() in graphite package
Pathways
Breast
siggenes
PROcess
cycle
graphite
Pathways
Breast
siggenes
PROcess
cycle
updated 11.2 years ago by
Enrica
▴ 20 • written 11.2 years ago by
array chip
▴ 420
0
votes
3
replies
1.5k
views
Most diff exp genes are up-regulated... can this be true?
Microarray
Normalization
vsn
limma
siggenes
Microarray
Normalization
vsn
limma
siggenes
11.4 years ago
Peter Davidsen
▴ 210
0
votes
0
replies
1.1k
views
converting intensity values to log ratios?
multtest
limma
siggenes
convert
multtest
limma
siggenes
convert
12.3 years ago
James W. MacDonald
65k
0
votes
3
replies
1.2k
views
Combining GEOquery with samr or siggenes
siggenes
GEOquery
siggenes
GEOquery
12.7 years ago
Voke AO
▴ 760
0
votes
1
reply
1.2k
views
siggenes parameters
siggenes
siggenes
12.8 years ago
Assa Yeroslaviz
★ 1.5k
0
votes
1
reply
1.2k
views
siggenes parameters
miRNA
siggenes
miRNA
siggenes
updated 12.9 years ago by
Holger Schwender
▴ 900 • written 12.9 years ago by
Assa Yeroslaviz
★ 1.5k
0
votes
0
replies
1.1k
views
miRNA microarray analysis
miRNA
affy
siggenes
miRNA
affy
siggenes
12.9 years ago
Assa Yeroslaviz
★ 1.5k
0
votes
1
reply
1.1k
views
understanding siggenes results
miRNA
affy
siggenes
miRNA
affy
siggenes
updated 13.0 years ago by
James W. MacDonald
65k • written 13.0 years ago by
Assa Yeroslaviz
★ 1.5k
0
votes
2
replies
1.2k
views
prepare data matrix for siggenes
siggenes
siggenes
updated 13.1 years ago by
Holger Schwender
▴ 900 • written 13.1 years ago by
joseph
▴ 330
0
votes
2
replies
2.0k
views
samr - extract genes from siggenes.table
siggenes
siggenes
updated 13.2 years ago by
Manca Marco PATH
▴ 340 • written 13.2 years ago by
Assa Yeroslaviz
★ 1.5k
0
votes
1
reply
1.7k
views
Help with GSEA package
hu6800
cdf
genefilter
multtest
affy
gcrma
siggenes
annaffy
GSEABase
hu6800
cdf
multtest
updated 13.4 years ago by
Martin Morgan
25k • written 13.4 years ago by
Jillian Rowe
▴ 20
0
votes
4
replies
2.1k
views
How is fold change reported in the samr output?
siggenes
impute
siggenes
impute
updated 13.6 years ago by
James W. MacDonald
65k • written 13.6 years ago by
brian snail
▴ 20
0
votes
0
replies
816
views
doubt about samr siggenes.table$genes.up
siggenes
siggenes
14.0 years ago
Leonardo Kenji Shikida
▴ 90
0
votes
5
replies
1.4k
views
normalisation + sam
Preprocessing
siggenes
Preprocessing
siggenes
updated 14.0 years ago by
Wolfgang Huber
★ 13k • written 14.0 years ago by
Mike Dewar
▴ 60
0
votes
1
reply
1.3k
views
Changes in siggenes?
Prostate
hgu133a2
probe
affy
siggenes
ASSIGN
Prostate
hgu133a2
probe
affy
siggenes
updated 14.3 years ago by
Holger Schwender
▴ 900 • written 14.3 years ago by
Torbjörn Klatt
▴ 10
0
votes
0
replies
852
views
lambda and other questions related to siggenes
GO
hgu133a
siggenes
GO
hgu133a
siggenes
14.4 years ago
John Lande
▴ 280
0
votes
1
reply
1.3k
views
samr package problems significant genes
siggenes
siggenes
updated 14.5 years ago by
Elana Fertig
▴ 10 • written 14.5 years ago by
Assa Yeroslaviz
★ 1.5k
0
votes
0
replies
873
views
Question about filtering genes when using siggenes
Annotation
genefilter
siggenes
Annotation
genefilter
siggenes
14.8 years ago
Manca Marco PATH
▴ 200
0
votes
1
reply
1.1k
views
R: Minor problem with siggenes's command sam2excel when entrez=TRUE
Annotation
siggenes
Annotation
siggenes
updated 14.8 years ago by
Holger Schwender
▴ 900 • written 14.8 years ago by
Manca Marco PATH
▴ 200
0
votes
1
reply
1.0k
views
Minor problem with siggenes's command sam2excel when entrez=TRUE
Annotation
siggenes
Annotation
siggenes
updated 14.8 years ago by
Holger Schwender
▴ 900 • written 14.8 years ago by
Manca Marco PATH
▴ 200
0
votes
2
replies
1.7k
views
R: Re: Thank you and small question - R: R: How to use GEOquery to extract more than the default information from a GSE
Annotation
limma
siggenes
GEOquery
Annotation
limma
siggenes
GEOquery
updated 14.8 years ago by
Sean Davis
21k • written 14.8 years ago by
Manca Marco PATH
▴ 200
0
votes
2
replies
2.9k
views
Random effects and variance components (was: Yet another nested design in limma)
affy
limma
siggenes
factDesign
maanova
affy
limma
siggenes
factDesign
maanova
updated 14.9 years ago by
James W. MacDonald
65k • written 14.9 years ago by
Paolo Innocenti
▴ 320
0
votes
2
replies
2.7k
views
Yet another nested design in limma
affy
limma
siggenes
factDesign
maanova
affy
limma
siggenes
factDesign
maanova
updated 15.0 years ago by
Paolo Innocenti
▴ 320 • written 15.0 years ago by
Gordon Smyth
50k
0
votes
0
replies
1.1k
views
Yet another nested design in limma
affy
limma
siggenes
factDesign
maanova
affy
limma
siggenes
factDesign
maanova
15.0 years ago
Paolo Innocenti
▴ 320
0
votes
1
reply
1.8k
views
Bug in topGO-package [topGO_1.10.0: GenTable-function]
GO
hgu133plus2
siggenes
GO
hgu133plus2
siggenes
updated 15.5 years ago by
Adrian Alexa
▴ 400 • written 15.5 years ago by
Samuel Wuest
▴ 330
0
votes
1
reply
988
views
Problem with analysis of paired data using Illumina arrays and the Lumi and limma packages
probe
siggenes
lumi
probe
siggenes
lumi
updated 15.6 years ago by
James W. MacDonald
65k • written 15.6 years ago by
Groeneweg M PATH
▴ 10
0
votes
0
replies
599
views
array weights in siggenes
siggenes
siggenes
15.8 years ago
Payton, Rebecca R
▴ 10
0
votes
0
replies
948
views
Two class paired analysis using siggenes
siggenes
siggenes
15.8 years ago
Mary Winn
▴ 10
0
votes
3
replies
2.3k
views
SAM analysis : samr package vs siggenes package
siggenes
siggenes
updated 16.0 years ago by
Holger Schwender
▴ 900 • written 16.0 years ago by
Cécile Laurent
▴ 30
0
votes
0
replies
904
views
trouble extracting R code from vignette using example from www.bioconductor.org
siggenes
siggenes
16.7 years ago
Kimpel, Mark W
▴ 890
1
vote
8
replies
7.1k
views
Limma, SAM and Fold Change Calculation
affy
limma
gcrma
siggenes
updated 7.1 years ago by
Gordon Smyth
50k • written 16.8 years ago by
Peter White
▴ 80
0
votes
0
replies
816
views
Note in check report was: [Bioc-devel] Recent changes in R
Cancer
annotate
genefilter
siggenes
Cancer
annotate
genefilter
siggenes
17.0 years ago
Seth Falcon
★ 7.4k
0
votes
3
replies
2.0k
views
hyperGTest, KEGG
Annotation
Pathways
multtest
siggenes
RBGL
GOstats
Annotation
Pathways
multtest
siggenes
updated 17.1 years ago by
Seth Falcon
★ 7.4k • written 17.1 years ago by
ivan.borozan@utoronto.ca
▴ 80
0
votes
1
reply
1.3k
views
[R] Why SAM has totally diffent results in R2.1.1 and R2.4.0
Microarray
Genetics
Survival
multtest
siggenes
safe
Microarray
Genetics
Survival
multtest
updated 17.5 years ago by
Holger Schwender
▴ 900 • written 17.5 years ago by
Martin Morgan
25k
0
votes
0
replies
797
views
SAM with censored survival data on exprSet
Survival
siggenes
Survival
siggenes
17.6 years ago
mpg33@drexel.edu
▴ 90
0
votes
0
replies
860
views
siggenes R-fold question
siggenes
siggenes
17.8 years ago
wxu@msi.umn.edu
▴ 220
0
votes
4
replies
1.1k
views
Communicating gene-probe relationships to sam
SNP
Biobase
siggenes
SNP
Biobase
siggenes
18.0 years ago
Charles Crane
▴ 30
0
votes
1
reply
1.0k
views
SAM and siggenes: 4 questions
siggenes
siggenes
updated 18.1 years ago by
Holger Schwender
▴ 900 • written 18.1 years ago by
Mohammad Esad-Djou
▴ 520
0
votes
4
replies
1.4k
views
siggenes error message about sam.plot2
siggenes
siggenes
18.1 years ago
He, Yiwen NIH/CIT
▴ 360
0
votes
1
reply
1.5k
views
SAM output explanation and an FDR question
siggenes
siggenes
updated 18.3 years ago by
Naomi Altman
★ 6.0k • written 18.3 years ago by
Ettinger, Nicholas
▴ 110
0
votes
2
replies
1.1k
views
siggenes permutation count problem
Normalization
affy
siggenes
Normalization
affy
siggenes
updated 18.3 years ago by
James W. MacDonald
65k • written 18.3 years ago by
Paul Boutros
▴ 340
0
votes
4
replies
1.4k
views
how to get samoutput$mat.fdr and samoutput$delta from SAM object ? - help
siggenes
siggenes
updated 18.4 years ago by
Sean Davis
21k • written 18.4 years ago by
SAURIN
★ 1.1k
0
votes
0
replies
728
views
called genes after SAM anaylsis
siggenes
siggenes
18.5 years ago
Holger Schwender
▴ 900
0
votes
3
replies
1.1k
views
attributes of SAM files
GUI
siggenes
GUI
siggenes
updated 18.5 years ago by
James W. MacDonald
65k • written 18.5 years ago by
Assa Yeroslaviz
▴ 100
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Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Chris
• 0
Intent to delete when going home. Sorry for that!
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Gordon Smyth
50k
Please ask you own question. Inserting your own dataset into someone else's question like this is very impolite. I have already answered m…
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: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Chris
• 0
Thanks Gordon for the advice!
Votes
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
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
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