Showing : siggenes • reset
1
vote
8
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7.4k
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Limma, SAM and Fold Change Calculation
affy limma gcrma siggenes
updated 7.7 years ago by 52k • written 17.5 years ago by ▴ 80
2
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2
replies
1.6k
views
SAM/siggenes: Differential gene expression analysis
SAM siggenes microarray gene expression sam
7.9 years ago Brian Smith ▴ 120
1
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0
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2.0k
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DE analysis of PCR array [was: dataset dim for siggenes]
qPCR Normalization multtest limma siggenes
10.3 years ago • updated 8.0 years ago Gordon Smyth 52k
2
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4
replies
1.5k
views
Interprentation of appropriate statistical test
samr SAM siggenes bioconductor differential gene expression
9.9 years ago svlachavas ▴ 840
0
votes
5
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1.7k
views
dataset dim for siggenes
qPCR limma siggenes
updated 10.3 years ago by 67k • written 10.3 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 10.3 years ago by 67k • written 10.3 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 11.5 years ago by ★ 13k • written 11.5 years ago by ★ 13k
0
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3
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2.2k
views
runSPIA() in graphite package
Pathways Breast siggenes PROcess cycle graphite Pathways Breast siggenes PROcess cycle
updated 11.9 years ago by ▴ 20 • written 11.9 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
12.0 years ago Peter Davidsen ▴ 210
0
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0
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1.2k
views
converting intensity values to log ratios?
multtest limma siggenes convert multtest limma siggenes convert
12.9 years ago James W. MacDonald 67k
0
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3
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1.3k
views
Combining GEOquery with samr or siggenes
siggenes GEOquery siggenes GEOquery
13.3 years ago Voke AO ▴ 760
0
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1
reply
1.3k
views
siggenes parameters
siggenes siggenes
13.5 years ago Assa Yeroslaviz ★ 1.5k
0
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1
reply
1.3k
views
siggenes parameters
miRNA siggenes miRNA siggenes
updated 13.5 years ago by ▴ 900 • written 13.5 years ago by ★ 1.5k
0
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0
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1.3k
views
miRNA microarray analysis
miRNA affy siggenes miRNA affy siggenes
13.5 years ago Assa Yeroslaviz ★ 1.5k
0
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1
reply
1.3k
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understanding siggenes results
miRNA affy siggenes miRNA affy siggenes
updated 13.6 years ago by 67k • written 13.6 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 13.7 years ago by ▴ 900 • written 13.7 years ago by ▴ 330
0
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2
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2.2k
views
samr - extract genes from siggenes.table
siggenes siggenes
updated 13.9 years ago by ▴ 340 • written 13.9 years ago by ★ 1.5k
0
votes
1
reply
1.9k
views
Help with GSEA package
hu6800 cdf genefilter multtest affy gcrma siggenes annaffy GSEABase hu6800 cdf multtest
updated 14.1 years ago by 25k • written 14.1 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 14.3 years ago by 67k • written 14.3 years ago by ▴ 20
0
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0
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922
views
doubt about samr siggenes.table$genes.up
siggenes siggenes
14.6 years ago Leonardo Kenji Shikida ▴ 90
0
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5
replies
1.6k
views
normalisation + sam
Preprocessing siggenes Preprocessing siggenes
updated 14.7 years ago by ★ 13k • written 14.7 years ago by ▴ 60
0
votes
1
reply
1.4k
views
Changes in siggenes?
Prostate hgu133a2 probe affy siggenes ASSIGN Prostate hgu133a2 probe affy siggenes
updated 15.0 years ago by ▴ 900 • written 15.0 years ago by ▴ 10
0
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0
replies
971
views
lambda and other questions related to siggenes
GO hgu133a siggenes GO hgu133a siggenes
15.0 years ago John Lande ▴ 280
0
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1
reply
1.4k
views
samr package problems significant genes
siggenes siggenes
updated 15.1 years ago by ▴ 10 • written 15.1 years ago by ★ 1.5k
0
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0
replies
970
views
Question about filtering genes when using siggenes
Annotation genefilter siggenes Annotation genefilter siggenes
15.4 years ago Manca Marco PATH ▴ 200
0
votes
1
reply
1.2k
views
R: Minor problem with siggenes's command sam2excel when entrez=TRUE
Annotation siggenes Annotation siggenes
updated 15.4 years ago by ▴ 900 • written 15.4 years ago by ▴ 200
0
votes
1
reply
1.1k
views
Minor problem with siggenes's command sam2excel when entrez=TRUE
Annotation siggenes Annotation siggenes
updated 15.4 years ago by ▴ 900 • written 15.4 years ago by ▴ 200
0
votes
2
replies
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 15.4 years ago by 21k • written 15.4 years ago by ▴ 200
0
votes
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 15.6 years ago by 67k • written 15.6 years ago by ▴ 320
0
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2
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2.9k
views
Yet another nested design in limma
affy limma siggenes factDesign maanova affy limma siggenes factDesign maanova
updated 15.6 years ago by ▴ 320 • written 15.6 years ago by 52k
0
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0
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1.2k
views
Yet another nested design in limma
affy limma siggenes factDesign maanova affy limma siggenes factDesign maanova
15.6 years ago Paolo Innocenti ▴ 320
0
votes
1
reply
1.9k
views
Bug in topGO-package [topGO_1.10.0: GenTable-function]
GO hgu133plus2 siggenes GO hgu133plus2 siggenes
updated 16.1 years ago by ▴ 400 • written 16.1 years ago by ▴ 330
0
votes
1
reply
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 16.2 years ago by 67k • written 16.2 years ago by ▴ 10
0
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0
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691
views
array weights in siggenes
siggenes siggenes
16.4 years ago Payton, Rebecca R ▴ 10
0
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0
replies
1.1k
views
Two class paired analysis using siggenes
siggenes siggenes
16.4 years ago Mary Winn ▴ 10
0
votes
3
replies
2.6k
views
SAM analysis : samr package vs siggenes package
siggenes siggenes
updated 16.7 years ago by ▴ 900 • written 16.7 years ago by ▴ 30
0
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0
replies
994
views
trouble extracting R code from vignette using example from www.bioconductor.org
siggenes siggenes
17.3 years ago Kimpel, Mark W ▴ 890
0
votes
0
replies
907
views
Note in check report was: [Bioc-devel] Recent changes in R
Cancer annotate genefilter siggenes Cancer annotate genefilter siggenes
17.6 years ago Seth Falcon ★ 7.4k
0
votes
3
replies
2.2k
views
hyperGTest, KEGG
Annotation Pathways multtest siggenes RBGL GOstats Annotation Pathways multtest siggenes
updated 17.7 years ago by ★ 7.4k • written 17.7 years ago by ▴ 80
0
votes
1
reply
1.4k
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 18.1 years ago by ▴ 900 • written 18.1 years ago by 25k
0
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0
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910
views
SAM with censored survival data on exprSet
Survival siggenes Survival siggenes
18.2 years ago mpg33@drexel.edu ▴ 90
0
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0
replies
963
views
siggenes R-fold question
siggenes siggenes
18.4 years ago wxu@msi.umn.edu ▴ 220
0
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4
replies
1.3k
views
Communicating gene-probe relationships to sam
SNP Biobase siggenes SNP Biobase siggenes
18.6 years ago Charles Crane ▴ 30
0
votes
1
reply
1.1k
views
SAM and siggenes: 4 questions
siggenes siggenes
updated 18.7 years ago by ▴ 900 • written 18.8 years ago by ▴ 520
0
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4
replies
1.6k
views
siggenes error message about sam.plot2
siggenes siggenes
18.8 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 19.0 years ago by ★ 6.0k • written 19.0 years ago by ▴ 110
0
votes
2
replies
1.3k
views
siggenes permutation count problem
Normalization affy siggenes Normalization affy siggenes
updated 19.0 years ago by 67k • written 19.0 years ago by ▴ 340
0
votes
4
replies
1.6k
views
how to get samoutput$mat.fdr and samoutput$delta from SAM object ? - help
siggenes siggenes
updated 19.0 years ago by 21k • written 19.0 years ago by ★ 1.1k
0
votes
0
replies
854
views
called genes after SAM anaylsis
siggenes siggenes
19.1 years ago Holger Schwender ▴ 900
0
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3
replies
1.3k
views
attributes of SAM files
GUI siggenes GUI siggenes
updated 19.1 years ago by 67k • written 19.1 years ago by ▴ 100
50 results • Page 1 of 1
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Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0
Thanks for your reply!
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C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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