Showing : siggenes • reset
1
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8
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Limma, SAM and Fold Change Calculation
affy limma gcrma siggenes
updated 8.7 years ago by 53k • written 18.4 years ago by ▴ 80
2
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2
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1.9k
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SAM/siggenes: Differential gene expression analysis
SAM siggenes microarray gene expression sam
8.9 years ago Brian Smith ▴ 120
1
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0
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2.3k
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DE analysis of PCR array [was: dataset dim for siggenes]
qPCR Normalization multtest limma siggenes
11.2 years ago • updated 8.9 years ago Gordon Smyth 53k
2
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4
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1.7k
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Interprentation of appropriate statistical test
samr SAM siggenes bioconductor differential gene expression
10.8 years ago svlachavas ▴ 840
0
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5
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1.9k
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dataset dim for siggenes
qPCR limma siggenes
updated 11.2 years ago by 68k • written 11.2 years ago by ▴ 100
0
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1
reply
1.7k
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SAM analysis of two color microarray data
Normalization limma siggenes
updated 11.2 years ago by 68k • written 11.2 years ago by ★ 13k
0
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1
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1.6k
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Unexpected results of differential expression analysis
GO limma siggenes GO limma siggenes
updated 12.4 years ago by ★ 13k • written 12.4 years ago by ★ 13k
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3
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2.5k
views
runSPIA() in graphite package
Pathways Breast siggenes PROcess cycle graphite Pathways Breast siggenes PROcess cycle
updated 12.8 years ago by ▴ 20 • written 12.8 years ago by ▴ 420
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3
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1.9k
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Most diff exp genes are up-regulated... can this be true?
Microarray Normalization vsn limma siggenes Microarray Normalization vsn limma siggenes
13.0 years ago Peter Davidsen ▴ 210
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1.4k
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converting intensity values to log ratios?
multtest limma siggenes convert multtest limma siggenes convert
13.8 years ago James W. MacDonald 68k
0
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3
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1.6k
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Combining GEOquery with samr or siggenes
siggenes GEOquery siggenes GEOquery
14.3 years ago Voke AO ▴ 760
0
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1
reply
1.5k
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siggenes parameters
siggenes siggenes
14.4 years ago Assa Yeroslaviz ★ 1.5k
0
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1
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1.5k
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siggenes parameters
miRNA siggenes miRNA siggenes
updated 14.4 years ago by ▴ 900 • written 14.4 years ago by ★ 1.5k
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0
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1.4k
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miRNA microarray analysis
miRNA affy siggenes miRNA affy siggenes
14.5 years ago Assa Yeroslaviz ★ 1.5k
0
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1
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1.4k
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understanding siggenes results
miRNA affy siggenes miRNA affy siggenes
updated 14.5 years ago by 68k • written 14.5 years ago by ★ 1.5k
0
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2
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1.5k
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prepare data matrix for siggenes
siggenes siggenes
updated 14.7 years ago by ▴ 900 • written 14.7 years ago by ▴ 330
0
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2
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2.4k
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samr - extract genes from siggenes.table
siggenes siggenes
updated 14.8 years ago by ▴ 340 • written 14.8 years ago by ★ 1.5k
0
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1
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2.1k
views
Help with GSEA package
hu6800 cdf genefilter multtest affy gcrma siggenes annaffy GSEABase hu6800 cdf multtest
updated 15.0 years ago by 25k • written 15.0 years ago by ▴ 20
0
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4
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2.6k
views
How is fold change reported in the samr output?
siggenes impute siggenes impute
updated 15.2 years ago by 68k • written 15.2 years ago by ▴ 20
0
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0
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1.0k
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doubt about samr siggenes.table$genes.up
siggenes siggenes
15.5 years ago Leonardo Kenji Shikida ▴ 90
0
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5
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1.8k
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normalisation + sam
Preprocessing siggenes Preprocessing siggenes
updated 15.6 years ago by ★ 13k • written 15.6 years ago by ▴ 60
0
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1
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1.6k
views
Changes in siggenes?
Prostate hgu133a2 probe affy siggenes ASSIGN Prostate hgu133a2 probe affy siggenes
updated 15.9 years ago by ▴ 900 • written 15.9 years ago by ▴ 10
0
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0
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1.1k
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lambda and other questions related to siggenes
GO hgu133a siggenes GO hgu133a siggenes
16.0 years ago John Lande ▴ 280
0
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1
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1.6k
views
samr package problems significant genes
siggenes siggenes
updated 16.0 years ago by ▴ 10 • written 16.1 years ago by ★ 1.5k
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0
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1.1k
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Question about filtering genes when using siggenes
Annotation genefilter siggenes Annotation genefilter siggenes
16.3 years ago Manca Marco PATH ▴ 200
0
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1
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1.4k
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R: Minor problem with siggenes's command sam2excel when entrez=TRUE
Annotation siggenes Annotation siggenes
updated 16.3 years ago by ▴ 900 • written 16.3 years ago by ▴ 200
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1
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1.3k
views
Minor problem with siggenes's command sam2excel when entrez=TRUE
Annotation siggenes Annotation siggenes
updated 16.3 years ago by ▴ 900 • written 16.3 years ago by ▴ 200
0
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2
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2.1k
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 16.4 years ago by 21k • written 16.4 years ago by ▴ 200
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2
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3.2k
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Random effects and variance components (was: Yet another nested design in limma)
affy limma siggenes factDesign maanova affy limma siggenes factDesign maanova
updated 16.5 years ago by 68k • written 16.5 years ago by ▴ 320
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2
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3.1k
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Yet another nested design in limma
affy limma siggenes factDesign maanova affy limma siggenes factDesign maanova
updated 16.6 years ago by ▴ 320 • written 16.6 years ago by 53k
0
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0
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1.3k
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Yet another nested design in limma
affy limma siggenes factDesign maanova affy limma siggenes factDesign maanova
16.6 years ago Paolo Innocenti ▴ 320
0
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1
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2.1k
views
Bug in topGO-package [topGO_1.10.0: GenTable-function]
GO hgu133plus2 siggenes GO hgu133plus2 siggenes
updated 17.0 years ago by ▴ 400 • written 17.0 years ago by ▴ 330
0
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1
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1.2k
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Problem with analysis of paired data using Illumina arrays and the Lumi and limma packages
probe siggenes lumi probe siggenes lumi
updated 17.2 years ago by 68k • written 17.2 years ago by ▴ 10
0
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0
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809
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array weights in siggenes
siggenes siggenes
17.3 years ago Payton, Rebecca R ▴ 10
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0
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1.2k
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Two class paired analysis using siggenes
siggenes siggenes
17.4 years ago Mary Winn ▴ 10
0
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3
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2.9k
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SAM analysis : samr package vs siggenes package
siggenes siggenes
updated 17.6 years ago by ▴ 900 • written 17.6 years ago by ▴ 30
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0
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1.1k
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trouble extracting R code from vignette using example from www.bioconductor.org
siggenes siggenes
18.3 years ago Kimpel, Mark W ▴ 890
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0
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1.0k
views
Note in check report was: [Bioc-devel] Recent changes in R
Cancer annotate genefilter siggenes Cancer annotate genefilter siggenes
18.6 years ago Seth Falcon ★ 7.4k
0
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3
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2.4k
views
hyperGTest, KEGG
Annotation Pathways multtest siggenes RBGL GOstats Annotation Pathways multtest siggenes
updated 18.6 years ago by ★ 7.4k • written 18.6 years ago by ▴ 80
0
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1
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1.6k
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 19.0 years ago by ▴ 900 • written 19.0 years ago by 25k
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0
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1.0k
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SAM with censored survival data on exprSet
Survival siggenes Survival siggenes
19.2 years ago mpg33@drexel.edu ▴ 90
0
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0
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1.1k
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siggenes R-fold question
siggenes siggenes
19.4 years ago wxu@msi.umn.edu ▴ 220
0
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4
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1.6k
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Communicating gene-probe relationships to sam
SNP Biobase siggenes SNP Biobase siggenes
19.6 years ago Charles Crane ▴ 30
0
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1
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1.3k
views
SAM and siggenes: 4 questions
siggenes siggenes
updated 19.7 years ago by ▴ 900 • written 19.7 years ago by ▴ 520
0
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4
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1.9k
views
siggenes error message about sam.plot2
siggenes siggenes
19.7 years ago He, Yiwen NIH/CIT ▴ 360
0
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1
reply
1.8k
views
SAM output explanation and an FDR question
siggenes siggenes
updated 19.9 years ago by ★ 6.0k • written 19.9 years ago by ▴ 110
0
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2
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1.4k
views
siggenes permutation count problem
Normalization affy siggenes Normalization affy siggenes
updated 19.9 years ago by 68k • written 19.9 years ago by ▴ 340
0
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4
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1.8k
views
how to get samoutput$mat.fdr and samoutput$delta from SAM object ? - help
siggenes siggenes
updated 20.0 years ago by 21k • written 20.0 years ago by ★ 1.1k
0
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0
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990
views
called genes after SAM anaylsis
siggenes siggenes
20.1 years ago Holger Schwender ▴ 900
0
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3
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1.5k
views
attributes of SAM files
GUI siggenes GUI siggenes
updated 20.1 years ago by 68k • written 20.1 years ago by ▴ 100
80 results • Page 1 of 2
Recent ...
Replies
Comment: problem reading bam files into nucleR by efoss ▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma by Gordon Smyth 53k
Answered here: https://support.bioconductor.org/p/16318/
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much! will take that into consideration
Comment: Large logFC but somewhat high FDR by JKim • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Comment: upstream git branches of bioc-release by Jeroen ▴ 10
OK I have updated https://bioc-release.r-universe.dev accordingly. Let me know if you find version differences when mirroring binaries.
Votes
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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