Showing : siggenes • reset
2
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4
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1.3k
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Interprentation of appropriate statistical test
samr SAM siggenes bioconductor differential gene expression
9.2 years ago svlachavas ▴ 830
2
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2
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1.4k
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SAM/siggenes: Differential gene expression analysis
SAM siggenes microarray gene expression sam
7.3 years ago Brian Smith ▴ 120
1
vote
8
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7.1k
views
Limma, SAM and Fold Change Calculation
affy limma gcrma siggenes
updated 7.1 years ago by 50k • written 16.8 years ago by ▴ 80
1
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0
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1.8k
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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
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2
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2.0k
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samr - extract genes from siggenes.table
siggenes siggenes
updated 13.2 years ago by ▴ 340 • written 13.2 years ago by ★ 1.5k
0
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1
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1.1k
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understanding siggenes results
miRNA affy siggenes miRNA affy siggenes
updated 13.0 years ago by 65k • written 13.0 years ago by ★ 1.5k
0
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1
reply
1.2k
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siggenes parameters
siggenes siggenes
12.8 years ago Assa Yeroslaviz ★ 1.5k
0
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0
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890
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Bioconductor
Microarray Normalization Cancer multtest siggenes convert Microarray Normalization Cancer
20.5 years ago James W. MacDonald 65k
0
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1
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1.0k
views
SAM in siggenes package
Microarray Cancer siggenes Microarray Cancer siggenes
updated 20.4 years ago by ▴ 900 • written 20.4 years ago by 65k
0
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1
reply
1.0k
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SAM output in siggenes package
siggenes siggenes
updated 20.4 years ago by 65k • written 20.4 years ago by ▴ 90
0
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7
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1.7k
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Statistical comparison of low replicate affy data
affy gcrma siggenes LPE affy gcrma siggenes LPE
20.2 years ago Matthew Hannah ▴ 940
0
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2
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1.4k
views
warning messages in gcrma
Microarray Normalization Cancer moe430a moe430b cdf probe affy gcrma siggenes GeneSpring
updated 20.1 years ago by 65k • written 20.1 years ago by ▴ 210
0
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3
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994
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SAM : warning messages problem
siggenes siggenes
updated 20.1 years ago by 65k • written 20.1 years ago by ▴ 90
0
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3
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1.1k
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Confusion for choosing package for microarray data analysis
Microarray limma siggenes marray Microarray limma siggenes marray
updated 20.1 years ago by ▴ 140 • written 20.1 years ago by ▴ 60
0
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0
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786
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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
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0
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963
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SAM: the fudge factor in Siggenes and Excel
siggenes ASSIGN siggenes ASSIGN
19.7 years ago Caimiao Wei ▴ 100
0
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4
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1.1k
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using mat.samp in siggenes
siggenes siggenes
updated 19.6 years ago by ▴ 900 • written 19.6 years ago by ▴ 20
0
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3
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1.0k
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about siggenes
siggenes siggenes
updated 19.6 years ago by ▴ 900 • written 19.6 years ago by ▴ 20
0
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0
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724
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calling SAM using siggenes package
siggenes siggenes
19.5 years ago saran.2.vardhanabhuti@gsk.com ▴ 10
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2
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1.3k
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gregmisc package-problems with BioC latest release?
Biobase annotate edd genefilter geneplotter ROC limma siggenes affyPLM marray Biobase
updated 19.5 years ago by ★ 7.4k • written 19.5 years ago by ▴ 130
0
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0
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1.0k
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Questions of Significance Analysis of Microarrays(SAM){siggenes}
siggenes siggenes
19.4 years ago yzu ▴ 10
0
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0
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903
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Questions of Significance Analysis of Microarrays(SAM){siggenes}
siggenes siggenes
19.4 years ago Holger Schwender ▴ 900
0
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0
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689
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Siggenes output only gives NAs?
siggenes siggenes
19.4 years ago Tiago R Magalhaes ▴ 60
0
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1
reply
946
views
Error message from running SAM for one-class case(siggenes)
siggenes siggenes
19.3 years ago Fangxin Hong ▴ 810
0
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3
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1.1k
views
problem with siggenes
Pharmacogenomics siggenes Pharmacogenomics siggenes
updated 19.3 years ago by ▴ 900 • written 19.3 years ago by ▴ 130
0
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2
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2.7k
views
Could you help me
siggenes siggenes
updated 19.3 years ago by ▴ 900 • written 19.3 years ago by ▴ 10
0
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0
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668
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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
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1
reply
997
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annotation problem with hgu133plus2
Annotation GO hgu133plus2 cdf annotate affy siggenes annaffy Annotation GO hgu133plus2
19.0 years ago • updated 18.9 years ago Yanqin Yang ▴ 250
0
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0
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837
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annotation problem with hgu133plus2
GO cdf annotate reposTools affy siggenes annaffy GO cdf annotate reposTools affy
19.0 years ago Seth Falcon ★ 7.4k
0
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1
reply
1.2k
views
siggenes SAM FDR, # false discrepancies
siggenes siggenes
18.9 years ago Jacob Michaelson ▴ 320
0
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0
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859
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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
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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 ★ 1.4k • written 18.8 years ago by ★ 1.1k
0
votes
1
reply
733
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Siggenes: How to deal with one treatment - five controls problem?
Microarray siggenes Microarray siggenes
updated 18.7 years ago by ▴ 190 • written 18.7 years ago by ▴ 10
0
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1
reply
840
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siggenes error with rma & wilcoxon test
siggenes siggenes
updated 18.6 years ago by ▴ 900 • written 18.6 years ago by ▴ 250
0
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3
replies
973
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passing my data to siggenes package
multtest siggenes multtest siggenes
updated 18.5 years ago by ▴ 900 • written 18.5 years ago by ▴ 140
0
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1
reply
763
views
siggenes package
siggenes siggenes
updated 18.5 years ago by ▴ 900 • written 18.5 years ago by ▴ 140
0
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3
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1.1k
views
attributes of SAM files
GUI siggenes GUI siggenes
updated 18.5 years ago by 65k • written 18.5 years ago by ▴ 100
0
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0
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725
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called genes after SAM anaylsis
siggenes siggenes
18.5 years ago Holger Schwender ▴ 900
0
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4
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1.4k
views
how to get samoutput$mat.fdr and samoutput$delta from SAM object ? - help
siggenes siggenes
updated 18.4 years ago by 21k • written 18.4 years ago by ★ 1.1k
0
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2
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1.1k
views
siggenes permutation count problem
Normalization affy siggenes Normalization affy siggenes
updated 18.3 years ago by 65k • written 18.3 years ago by ▴ 340
0
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1
reply
1.5k
views
SAM output explanation and an FDR question
siggenes siggenes
updated 18.3 years ago by ★ 6.0k • written 18.3 years ago by ▴ 110
0
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4
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1.4k
views
siggenes error message about sam.plot2
siggenes siggenes
18.1 years ago He, Yiwen NIH/CIT ▴ 360
0
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1
reply
1.0k
views
SAM and siggenes: 4 questions
siggenes siggenes
updated 18.1 years ago by ▴ 900 • written 18.1 years ago by ▴ 520
0
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0
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858
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siggenes R-fold question
siggenes siggenes
17.8 years ago wxu@msi.umn.edu ▴ 220
0
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0
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794
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SAM with censored survival data on exprSet
Survival siggenes Survival siggenes
17.6 years ago mpg33@drexel.edu ▴ 90
0
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3
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2.0k
views
hyperGTest, KEGG
Annotation Pathways multtest siggenes RBGL GOstats Annotation Pathways multtest siggenes
updated 17.1 years ago by ★ 7.4k • written 17.1 years ago by ▴ 80
0
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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
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
0
votes
5
replies
1.4k
views
normalisation + sam
Preprocessing siggenes Preprocessing siggenes
updated 14.0 years ago by ★ 13k • written 14.0 years ago by ▴ 60
0
votes
3
replies
2.3k
views
SAM analysis : samr package vs siggenes package
siggenes siggenes
updated 16.0 years ago by ▴ 900 • written 16.0 years ago by ▴ 30
50 results • Page 1 of 1
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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!
Comment: Too many significant genes when integrating gtex and tcga by Michael Love 41k
Yes, this was one of the aspects we highlighted in the 2014 paper, and it's also in the workflow. Check these places first. Also take a st…
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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