Showing : siggenes • reset
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
2
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4
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1.3k
views
Interprentation of appropriate statistical test
samr SAM siggenes bioconductor differential gene expression
9.2 years ago svlachavas ▴ 830
1
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0
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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
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5
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1.5k
views
dataset dim for siggenes
qPCR limma siggenes
updated 9.6 years ago by 65k • written 9.6 years ago by ▴ 100
0
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1
reply
1.3k
views
SAM analysis of two color microarray data
Normalization limma siggenes
updated 9.6 years ago by 65k • written 9.6 years ago by ★ 13k
0
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1
reply
1.2k
views
Unexpected results of differential expression analysis
GO limma siggenes GO limma siggenes
updated 10.8 years ago by ★ 13k • written 10.8 years ago by ★ 13k
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
0
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3
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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
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0
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1.1k
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converting intensity values to log ratios?
multtest limma siggenes convert multtest limma siggenes convert
12.2 years ago James W. MacDonald 65k
0
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3
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1.2k
views
Combining GEOquery with samr or siggenes
siggenes GEOquery siggenes GEOquery
12.7 years ago Voke AO ▴ 760
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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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
0
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0
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1.1k
views
miRNA microarray analysis
miRNA affy siggenes miRNA affy siggenes
12.9 years ago Assa Yeroslaviz ★ 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
0
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2
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1.2k
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prepare data matrix for siggenes
siggenes siggenes
updated 13.1 years ago by ▴ 900 • written 13.1 years ago by ▴ 330
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
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
0
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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
0
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0
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812
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doubt about samr siggenes.table$genes.up
siggenes siggenes
13.9 years ago Leonardo Kenji Shikida ▴ 90
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
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
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0
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842
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lambda and other questions related to siggenes
GO hgu133a siggenes GO hgu133a siggenes
14.4 years ago John Lande ▴ 280
0
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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
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0
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868
views
Question about filtering genes when using siggenes
Annotation genefilter siggenes Annotation genefilter siggenes
14.7 years ago Manca Marco PATH ▴ 200
0
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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
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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
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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
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2
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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
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2
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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 ▴ 320 • written 15.0 years ago by 50k
0
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0
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1.1k
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Yet another nested design in limma
affy limma siggenes factDesign maanova affy limma siggenes factDesign maanova
15.0 years ago Paolo Innocenti ▴ 320
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
votes
1
reply
983
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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0
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594
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array weights in siggenes
siggenes siggenes
15.7 years ago Payton, Rebecca R ▴ 10
0
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0
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942
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Two class paired analysis using siggenes
siggenes siggenes
15.8 years ago Mary Winn ▴ 10
0
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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
0
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0
replies
898
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 50k • written 16.8 years ago by ▴ 80
0
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0
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811
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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
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3
replies
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
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 17.4 years ago by ▴ 900 • written 17.4 years ago by 25k
0
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0
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786
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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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0
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853
views
siggenes R-fold question
siggenes siggenes
17.8 years ago wxu@msi.umn.edu ▴ 220
0
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4
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1.1k
views
Communicating gene-probe relationships to sam
SNP Biobase siggenes SNP Biobase siggenes
18.0 years ago Charles Crane ▴ 30
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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4
replies
1.4k
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siggenes error message about sam.plot2
siggenes siggenes
18.1 years ago He, Yiwen NIH/CIT ▴ 360
0
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1
reply
1.5k
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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2
replies
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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4
replies
1.4k
views
how to get samoutput$mat.fdr and samoutput$delta from SAM object ? - help
siggenes siggenes
updated 18.3 years ago by 21k • written 18.3 years ago by ★ 1.1k
0
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0
replies
717
views
called genes after SAM anaylsis
siggenes siggenes
18.5 years ago Holger Schwender ▴ 900
0
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3
replies
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
50 results • Page 1 of 1
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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?
Comment: minfi::read.metharray.exp by clacarion • 0
I think its work with `read.metharray.sheet` ```r > sheet <- read.metharray.sheet("/Users/clarachretienneau/Desktop/clock_epigenetic/PJ120…
Comment: minfi::read.metharray.exp by clacarion • 0
Thank you for your response Basti ! I add all the idat files in a unique folder called "idat" and add it in my path ```r > list.files("…
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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
Answer: Cannabis OrgDb
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