Showing : siggenes • reset
1
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8
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7.1k
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Limma, SAM and Fold Change Calculation
affy limma gcrma siggenes
updated 7.1 years ago by 50k • written 16.8 years ago by ▴ 80
2
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2
replies
1.4k
views
SAM/siggenes: Differential gene expression analysis
SAM siggenes microarray gene expression sam
7.3 years ago Brian Smith ▴ 120
1
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0
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1.8k
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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
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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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
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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
views
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
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1.1k
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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
views
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
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
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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
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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
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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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844
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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
1.3k
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
replies
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
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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
views
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
986
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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595
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array weights in siggenes
siggenes siggenes
15.7 years ago Payton, Rebecca R ▴ 10
0
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0
replies
942
views
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
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0
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898
views
trouble extracting R code from vignette using example from www.bioconductor.org
siggenes siggenes
16.7 years ago Kimpel, Mark W ▴ 890
0
votes
0
replies
812
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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
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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
votes
1
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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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787
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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
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siggenes R-fold question
siggenes siggenes
17.8 years ago wxu@msi.umn.edu ▴ 220
0
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4
replies
1.1k
views
Communicating gene-probe relationships to sam
SNP Biobase siggenes SNP Biobase siggenes
18.0 years ago Charles Crane ▴ 30
0
votes
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
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1.4k
views
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
votes
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
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1.4k
views
how to get samoutput$mat.fdr and samoutput$delta from SAM object ? - help
siggenes siggenes
updated 18.4 years ago by 21k • written 18.4 years ago by ★ 1.1k
0
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0
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718
views
called genes after SAM anaylsis
siggenes siggenes
18.5 years ago Holger Schwender ▴ 900
0
votes
3
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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
Recent ...
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Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR) by Michael Love 41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO by fernanda.backsouza ▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Answer: Opposite sign of LFC in count plots of DEGs (DESeq2) by swbarnes2 ★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error by James W. MacDonald 65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Votes
C: when to apply quantile normalization with voom in limma/voom framework with RNA-
A: How to know if I should use voomWithQualityWeights() or not?
A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom
Answer: Log-cpm values from limma
Answer: Log-cpm values from limma
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