Showing : siggenes • reset
1
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Limma, SAM and Fold Change Calculation
affy limma gcrma siggenes
updated 7.9 years ago by 52k • written 17.7 years ago by ▴ 80
2
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2
replies
1.7k
views
SAM/siggenes: Differential gene expression analysis
SAM siggenes microarray gene expression sam
8.1 years ago Brian Smith ▴ 120
1
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0
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2.1k
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DE analysis of PCR array [was: dataset dim for siggenes]
qPCR Normalization multtest limma siggenes
10.5 years ago • updated 8.2 years ago Gordon Smyth 52k
2
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4
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1.6k
views
Interprentation of appropriate statistical test
samr SAM siggenes bioconductor differential gene expression
10.1 years ago svlachavas ▴ 840
0
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5
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1.7k
views
dataset dim for siggenes
qPCR limma siggenes
updated 10.5 years ago by 68k • written 10.5 years ago by ▴ 100
0
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1
reply
1.5k
views
SAM analysis of two color microarray data
Normalization limma siggenes
updated 10.5 years ago by 68k • written 10.5 years ago by ★ 13k
0
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1
reply
1.4k
views
Unexpected results of differential expression analysis
GO limma siggenes GO limma siggenes
updated 11.7 years ago by ★ 13k • written 11.7 years ago by ★ 13k
0
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3
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2.3k
views
runSPIA() in graphite package
Pathways Breast siggenes PROcess cycle graphite Pathways Breast siggenes PROcess cycle
updated 12.1 years ago by ▴ 20 • written 12.1 years ago by ▴ 420
0
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3
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1.7k
views
Most diff exp genes are up-regulated... can this be true?
Microarray Normalization vsn limma siggenes Microarray Normalization vsn limma siggenes
12.2 years ago Peter Davidsen ▴ 210
0
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0
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1.3k
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converting intensity values to log ratios?
multtest limma siggenes convert multtest limma siggenes convert
13.1 years ago James W. MacDonald 68k
0
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3
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1.4k
views
Combining GEOquery with samr or siggenes
siggenes GEOquery siggenes GEOquery
13.5 years ago Voke AO ▴ 760
0
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1
reply
1.4k
views
siggenes parameters
siggenes siggenes
13.7 years ago Assa Yeroslaviz ★ 1.5k
0
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1
reply
1.4k
views
siggenes parameters
miRNA siggenes miRNA siggenes
updated 13.7 years ago by ▴ 900 • written 13.7 years ago by ★ 1.5k
0
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0
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1.3k
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miRNA microarray analysis
miRNA affy siggenes miRNA affy siggenes
13.7 years ago Assa Yeroslaviz ★ 1.5k
0
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1
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1.3k
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understanding siggenes results
miRNA affy siggenes miRNA affy siggenes
updated 13.8 years ago by 68k • written 13.8 years ago by ★ 1.5k
0
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2
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1.4k
views
prepare data matrix for siggenes
siggenes siggenes
updated 13.9 years ago by ▴ 900 • written 13.9 years ago by ▴ 330
0
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2
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2.3k
views
samr - extract genes from siggenes.table
siggenes siggenes
updated 14.1 years ago by ▴ 340 • written 14.1 years ago by ★ 1.5k
0
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1
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1.9k
views
Help with GSEA package
hu6800 cdf genefilter multtest affy gcrma siggenes annaffy GSEABase hu6800 cdf multtest
updated 14.3 years ago by 25k • written 14.3 years ago by ▴ 20
0
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4
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2.4k
views
How is fold change reported in the samr output?
siggenes impute siggenes impute
updated 14.5 years ago by 68k • written 14.5 years ago by ▴ 20
0
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0
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947
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doubt about samr siggenes.table$genes.up
siggenes siggenes
14.8 years ago Leonardo Kenji Shikida ▴ 90
0
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5
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1.6k
views
normalisation + sam
Preprocessing siggenes Preprocessing siggenes
updated 14.9 years ago by ★ 13k • written 14.9 years ago by ▴ 60
0
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1
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1.4k
views
Changes in siggenes?
Prostate hgu133a2 probe affy siggenes ASSIGN Prostate hgu133a2 probe affy siggenes
updated 15.2 years ago by ▴ 900 • written 15.2 years ago by ▴ 10
0
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0
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1.0k
views
lambda and other questions related to siggenes
GO hgu133a siggenes GO hgu133a siggenes
15.2 years ago John Lande ▴ 280
0
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1
reply
1.4k
views
samr package problems significant genes
siggenes siggenes
updated 15.3 years ago by ▴ 10 • written 15.3 years ago by ★ 1.5k
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0
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1.0k
views
Question about filtering genes when using siggenes
Annotation genefilter siggenes Annotation genefilter siggenes
15.6 years ago Manca Marco PATH ▴ 200
0
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1
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1.3k
views
R: Minor problem with siggenes's command sam2excel when entrez=TRUE
Annotation siggenes Annotation siggenes
updated 15.6 years ago by ▴ 900 • written 15.6 years ago by ▴ 200
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1
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1.2k
views
Minor problem with siggenes's command sam2excel when entrez=TRUE
Annotation siggenes Annotation siggenes
updated 15.6 years ago by ▴ 900 • written 15.6 years ago by ▴ 200
0
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2
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1.9k
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 15.6 years ago by 21k • written 15.6 years ago by ▴ 200
0
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2
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3.0k
views
Random effects and variance components (was: Yet another nested design in limma)
affy limma siggenes factDesign maanova affy limma siggenes factDesign maanova
updated 15.8 years ago by 68k • written 15.8 years ago by ▴ 320
0
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2
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2.9k
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Yet another nested design in limma
affy limma siggenes factDesign maanova affy limma siggenes factDesign maanova
updated 15.8 years ago by ▴ 320 • written 15.8 years ago by 52k
0
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0
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1.2k
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Yet another nested design in limma
affy limma siggenes factDesign maanova affy limma siggenes factDesign maanova
15.8 years ago Paolo Innocenti ▴ 320
0
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1
reply
2.0k
views
Bug in topGO-package [topGO_1.10.0: GenTable-function]
GO hgu133plus2 siggenes GO hgu133plus2 siggenes
updated 16.3 years ago by ▴ 400 • written 16.3 years ago by ▴ 330
0
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1
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1.1k
views
Problem with analysis of paired data using Illumina arrays and the Lumi and limma packages
probe siggenes lumi probe siggenes lumi
updated 16.4 years ago by 68k • written 16.4 years ago by ▴ 10
0
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0
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717
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array weights in siggenes
siggenes siggenes
16.6 years ago Payton, Rebecca R ▴ 10
0
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0
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1.1k
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Two class paired analysis using siggenes
siggenes siggenes
16.6 years ago Mary Winn ▴ 10
0
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3
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2.7k
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SAM analysis : samr package vs siggenes package
siggenes siggenes
updated 16.9 years ago by ▴ 900 • written 16.9 years ago by ▴ 30
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0
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1.0k
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trouble extracting R code from vignette using example from www.bioconductor.org
siggenes siggenes
17.5 years ago Kimpel, Mark W ▴ 890
0
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0
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932
views
Note in check report was: [Bioc-devel] Recent changes in R
Cancer annotate genefilter siggenes Cancer annotate genefilter siggenes
17.8 years ago Seth Falcon ★ 7.4k
0
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3
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2.2k
views
hyperGTest, KEGG
Annotation Pathways multtest siggenes RBGL GOstats Annotation Pathways multtest siggenes
updated 17.9 years ago by ★ 7.4k • written 17.9 years ago by ▴ 80
0
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1
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1.5k
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 18.3 years ago by ▴ 900 • written 18.3 years ago by 25k
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0
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934
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SAM with censored survival data on exprSet
Survival siggenes Survival siggenes
18.4 years ago mpg33@drexel.edu ▴ 90
0
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0
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991
views
siggenes R-fold question
siggenes siggenes
18.6 years ago wxu@msi.umn.edu ▴ 220
0
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4
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1.3k
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Communicating gene-probe relationships to sam
SNP Biobase siggenes SNP Biobase siggenes
18.8 years ago Charles Crane ▴ 30
0
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1
reply
1.2k
views
SAM and siggenes: 4 questions
siggenes siggenes
updated 19.0 years ago by ▴ 900 • written 19.0 years ago by ▴ 520
0
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4
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1.7k
views
siggenes error message about sam.plot2
siggenes siggenes
19.0 years ago He, Yiwen NIH/CIT ▴ 360
0
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1
reply
1.6k
views
SAM output explanation and an FDR question
siggenes siggenes
updated 19.2 years ago by ★ 6.0k • written 19.2 years ago by ▴ 110
0
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2
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1.3k
views
siggenes permutation count problem
Normalization affy siggenes Normalization affy siggenes
updated 19.2 years ago by 68k • written 19.2 years ago by ▴ 340
0
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4
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1.6k
views
how to get samoutput$mat.fdr and samoutput$delta from SAM object ? - help
siggenes siggenes
updated 19.2 years ago by 21k • written 19.2 years ago by ★ 1.1k
0
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0
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883
views
called genes after SAM anaylsis
siggenes siggenes
19.3 years ago Holger Schwender ▴ 900
0
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3
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1.3k
views
attributes of SAM files
GUI siggenes GUI siggenes
updated 19.3 years ago by 68k • written 19.3 years ago by ▴ 100
50 results • Page 1 of 1
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Comment: Use of limma R package with targeted proteomics for DE analysis by svlachavas ▴ 840
Dear Gordon, thank you for returning back ! Actually the output is not "NPX"-as indeed it most frequent output for a lot of pannels-but as …
Comment: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k
If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…
Comment: Compare TCGA-PAAD with GTEx gene expression by Jane • 0
why aren't there any answers?
Comment: Too many significant genes when integrating gtex and tcga by Jane • 0
I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…
Comment: how many significant figures are there in DESeq2 output by Matthew McCormack ▴ 180
Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…
Votes
A: What is the "linear model" part used for in Limma?
Comment: Use of limma R package with targeted proteomics for DE analysis
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
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