Showing : siggenes • reset
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4
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siggenes error message about sam.plot2
siggenes siggenes
18.1 years ago He, Yiwen NIH/CIT ▴ 360
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4
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1.1k
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Communicating gene-probe relationships to sam
SNP Biobase siggenes SNP Biobase siggenes
18.0 years ago Charles Crane ▴ 30
0
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7
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1.6k
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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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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
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3
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991
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SAM : warning messages problem
siggenes siggenes
updated 20.1 years ago by 65k • written 20.1 years ago by ▴ 90
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3
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1.1k
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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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3
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966
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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
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3
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1.2k
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Combining GEOquery with samr or siggenes
siggenes GEOquery siggenes GEOquery
12.7 years ago Voke AO ▴ 760
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
0
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3
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1.9k
views
runSPIA() in graphite package
Pathways Breast siggenes PROcess cycle graphite Pathways Breast siggenes PROcess cycle
updated 11.2 years ago by ▴ 20 • written 11.2 years ago by ▴ 420
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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
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2
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2.7k
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Yet another nested design in limma
affy limma siggenes factDesign maanova affy limma siggenes factDesign maanova
updated 15.0 years ago by ▴ 320 • written 15.0 years ago by 50k
0
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2
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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 ★ 7.4k • written 19.5 years ago by ▴ 130
0
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5
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1.4k
views
normalisation + sam
Preprocessing siggenes Preprocessing siggenes
updated 14.0 years ago by ★ 13k • written 14.0 years ago by ▴ 60
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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 17.0 years ago by ★ 7.4k • written 17.0 years ago by ▴ 80
0
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2
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2.7k
views
Could you help me
siggenes siggenes
updated 19.2 years ago by ▴ 900 • written 19.2 years ago by ▴ 10
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
0
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3
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1.1k
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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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2
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1.4k
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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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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 ▴ 140 • written 20.1 years ago by ▴ 60
0
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1
reply
1.2k
views
siggenes parameters
miRNA siggenes miRNA siggenes
updated 12.8 years ago by ▴ 900 • written 12.8 years ago by ★ 1.5k
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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 17.4 years ago by ▴ 900 • written 17.4 years ago by 25k
0
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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 25k • written 13.4 years ago by ▴ 20
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2
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2.0k
views
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
reply
1.1k
views
understanding siggenes results
miRNA affy siggenes miRNA affy siggenes
updated 12.9 years ago by 65k • written 12.9 years ago by ★ 1.5k
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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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1
reply
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
views
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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1
reply
940
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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1
reply
989
views
annotation problem with hgu133plus2
Annotation GO hgu133plus2 cdf annotate affy siggenes annaffy Annotation GO hgu133plus2
18.9 years ago Yanqin Yang ▴ 250
0
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1
reply
1.2k
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siggenes SAM FDR, # false discrepancies
siggenes siggenes
18.9 years ago Jacob Michaelson ▴ 320
0
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1
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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
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1
reply
725
views
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
837
views
siggenes error with rma & wilcoxon test
siggenes siggenes
updated 18.5 years ago by ▴ 900 • written 18.5 years ago by ▴ 250
0
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1
reply
758
views
siggenes package
siggenes siggenes
updated 18.5 years ago by ▴ 900 • written 18.5 years ago by ▴ 140
0
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4
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1.4k
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how to get samoutput$mat.fdr and samoutput$delta from SAM object ? - help
siggenes siggenes
updated 18.3 years ago by 21k • written 18.4 years ago by ★ 1.1k
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2
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1.1k
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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
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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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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
1
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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
0
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3
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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
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 65k • written 14.9 years ago by ▴ 320
0
votes
1
reply
985
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 65k • written 15.6 years ago by ▴ 10
0
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1
reply
1.8k
views
Bug in topGO-package [topGO_1.10.0: GenTable-function]
GO hgu133plus2 siggenes GO hgu133plus2 siggenes
updated 15.4 years ago by ▴ 400 • written 15.4 years ago by ▴ 330
0
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2
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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 14.7 years ago by 21k • written 14.7 years ago by ▴ 200
0
votes
1
reply
1.0k
views
Minor problem with siggenes's command sam2excel when entrez=TRUE
Annotation siggenes Annotation siggenes
updated 14.7 years ago by ▴ 900 • written 14.7 years ago by ▴ 200
0
votes
1
reply
1.1k
views
R: Minor problem with siggenes's command sam2excel when entrez=TRUE
Annotation siggenes Annotation siggenes
updated 14.7 years ago by ▴ 900 • written 14.7 years ago by ▴ 200
0
votes
1
reply
1.2k
views
samr package problems significant genes
siggenes siggenes
updated 14.4 years ago by ▴ 10 • written 14.5 years ago by ★ 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 ▴ 900 • written 14.3 years ago by ▴ 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 65k • written 13.6 years ago by ▴ 20
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Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
How am i making the data? I am using the DESeq2 output data which I had generated
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq by Michael Love 41k
Sounds reasonable. For ranking genes, you could choose those with low decay rate but removing thoses where it is indistinguishable from …
Answer: Citation for edgeR user guide by Gordon Smyth 50k
Thanks for thinking about how to cite edgeR. Citations are indeed the main way by which the edgeR authors get credit for their work. The Us…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You are just making up data? What is the point of this exercise?
Comment: How to retrieve gene ontology GO class? by James W. MacDonald 65k
What do you mean by 'the information'? Do you have things in particular that you want?
Votes
Answer: Citation for edgeR user guide
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
Answer: How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
Answer: minfi::read.metharray.exp
Comment: Trying to use enrichGO
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