Showing : siggenes • reset
1
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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
0
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7
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1.7k
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Statistical comparison of low replicate affy data
affy gcrma siggenes LPE affy gcrma siggenes LPE
20.2 years ago Matthew Hannah ▴ 940
0
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5
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1.5k
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dataset dim for siggenes
qPCR limma siggenes
updated 9.7 years ago by 65k • written 9.7 years ago by ▴ 100
0
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5
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1.4k
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normalisation + sam
Preprocessing siggenes Preprocessing siggenes
updated 14.1 years ago by ★ 13k • written 14.1 years ago by ▴ 60
0
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4
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1.4k
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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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4
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1.1k
views
using mat.samp in siggenes
siggenes siggenes
updated 19.7 years ago by ▴ 900 • written 19.7 years ago by ▴ 20
0
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4
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2.1k
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How is fold change reported in the samr output?
siggenes impute siggenes impute
updated 13.7 years ago by 65k • written 13.7 years ago by ▴ 20
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
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
9.3 years ago svlachavas ▴ 830
0
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4
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1.1k
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Communicating gene-probe relationships to sam
SNP Biobase siggenes SNP Biobase siggenes
18.0 years ago Charles Crane ▴ 30
0
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3
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995
views
SAM : warning messages problem
siggenes siggenes
updated 20.2 years ago by 65k • written 20.2 years ago by ▴ 90
0
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3
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976
views
passing my data to siggenes package
multtest siggenes multtest siggenes
updated 18.5 years ago by ▴ 900 • written 18.5 years ago by ▴ 140
0
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3
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1.1k
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Confusion for choosing package for microarray data analysis
Microarray limma siggenes marray Microarray limma siggenes marray
updated 20.2 years ago by ▴ 140 • written 20.2 years ago by ▴ 60
0
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3
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1.1k
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attributes of SAM files
GUI siggenes GUI siggenes
updated 18.5 years ago by 65k • written 18.5 years ago by ▴ 100
0
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3
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2.3k
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SAM analysis : samr package vs siggenes package
siggenes siggenes
updated 16.1 years ago by ▴ 900 • written 16.1 years ago by ▴ 30
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 17.1 years ago by ★ 7.4k • written 17.1 years ago by ▴ 80
0
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3
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1.0k
views
about siggenes
siggenes siggenes
updated 19.7 years ago by ▴ 900 • written 19.7 years ago by ▴ 20
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 11.3 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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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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3
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1.1k
views
problem with siggenes
Pharmacogenomics siggenes Pharmacogenomics siggenes
updated 19.3 years ago by ▴ 900 • written 19.3 years ago by ▴ 130
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2
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2.0k
views
samr - extract genes from siggenes.table
siggenes siggenes
updated 13.3 years ago by ▴ 340 • written 13.3 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
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
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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2
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2.7k
views
Could you help me
siggenes siggenes
updated 19.3 years ago by ▴ 900 • written 19.3 years ago by ▴ 10
0
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2
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1.4k
views
warning messages in gcrma
Microarray Normalization Cancer moe430a moe430b cdf probe affy gcrma siggenes GeneSpring
updated 20.2 years ago by 65k • written 20.2 years ago by ▴ 210
0
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2
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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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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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1.3k
views
gregmisc package-problems with BioC latest release?
Biobase annotate edd genefilter geneplotter ROC limma siggenes affyPLM marray Biobase
updated 19.5 years ago by ★ 7.4k • written 19.5 years ago by ▴ 130
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 14.8 years ago by 21k • written 14.8 years ago by ▴ 200
0
votes
1
reply
1.2k
views
siggenes parameters
miRNA siggenes miRNA siggenes
updated 12.9 years ago by ▴ 900 • written 12.9 years ago by ★ 1.5k
0
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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 17.5 years ago by ▴ 900 • written 17.5 years ago by 25k
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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1
reply
1.1k
views
understanding siggenes results
miRNA affy siggenes miRNA affy siggenes
updated 13.0 years ago by 65k • written 13.0 years ago by ★ 1.5k
0
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1
reply
1.2k
views
siggenes parameters
siggenes siggenes
12.9 years ago Assa Yeroslaviz ★ 1.5k
0
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1
reply
1.0k
views
SAM in siggenes package
Microarray Cancer siggenes Microarray Cancer siggenes
updated 20.4 years ago by ▴ 900 • written 20.4 years ago by 65k
0
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1
reply
1.0k
views
SAM output in siggenes package
siggenes siggenes
updated 20.4 years ago by 65k • written 20.4 years ago by ▴ 90
0
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1
reply
949
views
Error message from running SAM for one-class case(siggenes)
siggenes siggenes
19.3 years ago Fangxin Hong ▴ 810
0
votes
1
reply
1000
views
annotation problem with hgu133plus2
Annotation GO hgu133plus2 cdf annotate affy siggenes annaffy Annotation GO hgu133plus2
19.0 years ago Yanqin Yang ▴ 250
0
votes
1
reply
1.2k
views
siggenes SAM FDR, # false discrepancies
siggenes siggenes
18.9 years ago Jacob Michaelson ▴ 320
0
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1
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1.1k
views
Error in qc.affy(unnormalised, ...) : I'm sorry, I do not know about chip type: moe430acdf
GO moe430a cdf reposTools limma gcrma matchprobes siggenes simpleaffy GO moe430a cdf
updated 18.8 years ago by ★ 1.4k • written 18.8 years ago by ★ 1.1k
0
votes
1
reply
733
views
Siggenes: How to deal with one treatment - five controls problem?
Microarray siggenes Microarray siggenes
updated 18.7 years ago by ▴ 190 • written 18.7 years ago by ▴ 10
0
votes
1
reply
842
views
siggenes error with rma & wilcoxon test
siggenes siggenes
updated 18.6 years ago by ▴ 900 • written 18.6 years ago by ▴ 250
0
votes
1
reply
764
views
siggenes package
siggenes siggenes
updated 18.5 years ago by ▴ 900 • written 18.5 years ago by ▴ 140
0
votes
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
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
votes
1
reply
988
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
votes
1
reply
1.8k
views
Bug in topGO-package [topGO_1.10.0: GenTable-function]
GO hgu133plus2 siggenes GO hgu133plus2 siggenes
updated 15.5 years ago by ▴ 400 • written 15.5 years ago by ▴ 330
0
votes
1
reply
1.0k
views
Minor problem with siggenes's command sam2excel when entrez=TRUE
Annotation siggenes Annotation siggenes
updated 14.8 years ago by ▴ 900 • written 14.8 years ago by ▴ 200
50 results • Page 1 of 1
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Replies
Comment: EGSEA usage with microarray data (with vooma)? by Chris • 0
Hi Pekka, I also try EGSEA with microarray data. However, I got this error. Would you please have a suggestion? gsa = egsea.ma(numeric…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
> Any suggestions for methylation data segmentation? I think the same segmentation can be used.
Comment: deseq2 results by swbarnes2 ★ 1.3k
Cross-posted https://www.biostars.org/p/9594331/#9594458
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by Mike Smith ★ 6.5k
The other answers here are all good and demonstrate the issue with floating point comparisons nicely. I'd like to add that your particular…
Comment: More regions in union when increasing DBA$config$mergeOverlap by Ian D. ▴ 70
Nudging my question. I could do with confirmation before proceeding with my current projects. Thank you.
Votes
A: Volcanoplot with limma - RAW P-values or Adj.P-Values
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: minfi latest update for EPIC V2 chip
A: Error in DESeqDataSet : some values in assay are not integers
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