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Showing :
siggenes
•
reset
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
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
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
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
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
0
replies
890
views
Bioconductor
Microarray
Normalization
Cancer
multtest
siggenes
convert
Microarray
Normalization
Cancer
20.5 years ago
James W. MacDonald
65k
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
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
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
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
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
0
replies
785
views
downstream analysis of differentially expressed genes
Microarray
Cancer
multtest
affy
limma
siggenes
factDesign
Microarray
Cancer
multtest
20.0 years ago
James W. MacDonald
65k
0
votes
0
replies
960
views
SAM: the fudge factor in Siggenes and Excel
siggenes
ASSIGN
siggenes
ASSIGN
19.7 years ago
Caimiao Wei
▴ 100
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
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
0
replies
724
views
calling SAM using siggenes package
siggenes
siggenes
19.5 years ago
saran.2.vardhanabhuti@gsk.com
▴ 10
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
0
replies
1.0k
views
Questions of Significance Analysis of Microarrays(SAM){siggenes}
siggenes
siggenes
19.4 years ago
yzu
▴ 10
0
votes
0
replies
902
views
Questions of Significance Analysis of Microarrays(SAM){siggenes}
siggenes
siggenes
19.4 years ago
Holger Schwender
▴ 900
0
votes
0
replies
689
views
Siggenes output only gives NAs?
siggenes
siggenes
19.4 years ago
Tiago R Magalhaes
▴ 60
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
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
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
0
votes
0
replies
665
views
Gene selection: association with linear response and correction for multi test
Regression
limma
siggenes
Regression
limma
siggenes
19.1 years ago
david neil hayes
▴ 70
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
0
replies
836
views
annotation problem with hgu133plus2
GO
cdf
annotate
reposTools
affy
siggenes
annaffy
GO
cdf
annotate
reposTools
affy
18.9 years ago
Seth Falcon
★ 7.4k
0
votes
1
reply
1.2k
views
siggenes SAM FDR, # false discrepancies
siggenes
siggenes
18.9 years ago
Jacob Michaelson
▴ 320
0
votes
0
replies
858
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
18.8 years ago
Dick Beyer
★ 1.4k
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
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
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
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
0
replies
723
views
called genes after SAM anaylsis
siggenes
siggenes
18.5 years ago
Holger Schwender
▴ 900
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
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
1.0k
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
0
replies
857
views
siggenes R-fold question
siggenes
siggenes
17.8 years ago
wxu@msi.umn.edu
▴ 220
0
votes
0
replies
791
views
SAM with censored survival data on exprSet
Survival
siggenes
Survival
siggenes
17.6 years ago
mpg33@drexel.edu
▴ 90
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
0
replies
815
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
0
replies
903
views
trouble extracting R code from vignette using example from www.bioconductor.org
siggenes
siggenes
16.7 years ago
Kimpel, Mark W
▴ 890
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
2.3k
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
50 results • Page
1 of 1
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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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