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Showing :
siggenes
•
reset
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
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
7
replies
1.7k
views
Statistical comparison of low replicate affy data
affy
gcrma
siggenes
LPE
affy
gcrma
siggenes
LPE
20.2 years ago
Matthew Hannah
▴ 940
0
votes
4
replies
1.1k
views
using mat.samp in siggenes
siggenes
siggenes
updated 19.6 years ago by
Holger Schwender
▴ 900 • written 19.6 years ago by
Kathleen Kerr
▴ 20
0
votes
3
replies
992
views
SAM : warning messages problem
siggenes
siggenes
updated 20.1 years ago by
James W. MacDonald
65k • written 20.1 years ago by
Willy Wynant
▴ 90
0
votes
3
replies
1.1k
views
problem with siggenes
Pharmacogenomics
siggenes
Pharmacogenomics
siggenes
updated 19.3 years ago by
Holger Schwender
▴ 900 • written 19.3 years ago by
Edoardo Saccenti
▴ 130
0
votes
3
replies
973
views
passing my data to siggenes package
multtest
siggenes
multtest
siggenes
updated 18.5 years ago by
Holger Schwender
▴ 900 • written 18.5 years ago by
madhurima bhattacharjee
▴ 140
0
votes
3
replies
1.2k
views
Combining GEOquery with samr or siggenes
siggenes
GEOquery
siggenes
GEOquery
12.7 years ago
Voke AO
▴ 760
2
votes
4
replies
1.3k
views
Interprentation of appropriate statistical test
samr
SAM
siggenes
bioconductor
differential gene expression
9.2 years ago
svlachavas
▴ 830
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
1.0k
views
about siggenes
siggenes
siggenes
updated 19.6 years ago by
Holger Schwender
▴ 900 • written 19.6 years ago by
haojie
▴ 20
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
2
replies
1.3k
views
gregmisc package-problems with BioC latest release?
Biobase
annotate
edd
genefilter
geneplotter
ROC
limma
siggenes
affyPLM
marray
Biobase
updated 19.5 years ago by
Seth Falcon
★ 7.4k • written 19.5 years ago by
Fátima Núñez
▴ 130
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
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
2
replies
2.7k
views
Could you help me
siggenes
siggenes
updated 19.2 years ago by
Holger Schwender
▴ 900 • written 19.2 years ago by
Liao, Guiping
▴ 10
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
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
0
votes
2
replies
1.4k
views
warning messages in gcrma
Microarray
Normalization
Cancer
moe430a
moe430b
cdf
probe
affy
gcrma
siggenes
GeneSpring
updated 20.1 years ago by
James W. MacDonald
65k • written 20.1 years ago by
Lizhe Xu
▴ 210
0
votes
3
replies
1.1k
views
Confusion for choosing package for microarray data analysis
Microarray
limma
siggenes
marray
Microarray
limma
siggenes
marray
updated 20.1 years ago by
Christopher Wilkinson
▴ 140 • written 20.1 years ago by
Yi Zou
▴ 60
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
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
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
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
1.1k
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
1
reply
1.2k
views
siggenes parameters
siggenes
siggenes
12.8 years ago
Assa Yeroslaviz
★ 1.5k
0
votes
1
reply
1.0k
views
SAM in siggenes package
Microarray
Cancer
siggenes
Microarray
Cancer
siggenes
updated 20.4 years ago by
Holger Schwender
▴ 900 • written 20.4 years ago by
James W. MacDonald
65k
0
votes
1
reply
1.0k
views
SAM output in siggenes package
siggenes
siggenes
updated 20.4 years ago by
James W. MacDonald
65k • written 20.4 years ago by
Anna Cao
▴ 90
0
votes
1
reply
943
views
Error message from running SAM for one-class case(siggenes)
siggenes
siggenes
19.3 years ago
Fangxin Hong
▴ 810
0
votes
1
reply
995
views
annotation problem with hgu133plus2
Annotation
GO
hgu133plus2
cdf
annotate
affy
siggenes
annaffy
Annotation
GO
hgu133plus2
18.9 years ago
Yanqin Yang
▴ 250
0
votes
1
reply
1.2k
views
siggenes SAM FDR, # false discrepancies
siggenes
siggenes
18.9 years ago
Jacob Michaelson
▴ 320
0
votes
1
reply
1.1k
views
Error in qc.affy(unnormalised, ...) : I'm sorry, I do not know about chip type: moe430acdf
GO
moe430a
cdf
reposTools
limma
gcrma
matchprobes
siggenes
simpleaffy
GO
moe430a
cdf
updated 18.8 years ago by
Dick Beyer
★ 1.4k • written 18.8 years ago by
Crispin Miller
★ 1.1k
0
votes
1
reply
731
views
Siggenes: How to deal with one treatment - five controls problem?
Microarray
siggenes
Microarray
siggenes
updated 18.7 years ago by
Norman Pavelka
▴ 190 • written 18.7 years ago by
Paolo Sirabella
▴ 10
0
votes
1
reply
840
views
siggenes error with rma & wilcoxon test
siggenes
siggenes
updated 18.6 years ago by
Holger Schwender
▴ 900 • written 18.6 years ago by
Ken Termiso
▴ 250
0
votes
1
reply
762
views
siggenes package
siggenes
siggenes
updated 18.5 years ago by
Holger Schwender
▴ 900 • written 18.5 years ago by
madhurima bhattacharjee
▴ 140
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
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
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
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
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
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
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
1
reply
987
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
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
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
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
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
1.3k
views
samr package problems significant genes
siggenes
siggenes
updated 14.4 years ago by
Elana Fertig
▴ 10 • written 14.5 years ago by
Assa Yeroslaviz
★ 1.5k
0
votes
1
reply
1.2k
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
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
50 results • Page
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Comment: log2FoldChange value is way too different when compared with counts(dds)
by
Michael Love
41k
But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
HAK
• 0
Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
ATpoint
★ 4.1k
Here the error probably means that you habe genes where expression scross all samples is the same. Rowscaling is value minus mean divided b…
Comment: Store output of matchPWM()
by
James W. MacDonald
65k
Here's a self contained reproducible example, using part of the example in `?matchPWM` ``` > library(Biostrings) > data(HNF4alpha) > libr…
Comment: DEseq2 coefficient
by
JKim
• 0
Hi Dr. Love, I'm sorry to ask another question to my old post. If the design isn't balanced, the interpretation of coefficients will be…
Votes
SPIA plotP giving error
Answer: Fold change calculation in Diffbind vs. DESEQ2?
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
C: Extremely big genes in annotation TxDb packages
Make custom Txdb class objects from Txdb
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