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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1.6k
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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
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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5
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1.4k
views
normalisation + sam
Preprocessing siggenes Preprocessing siggenes
updated 14.0 years ago by ★ 13k • written 14.0 years ago by ▴ 60
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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4
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1.1k
views
using mat.samp in siggenes
siggenes siggenes
updated 19.6 years ago by ▴ 900 • written 19.6 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 13.6 years ago by 65k • written 13.6 years ago by ▴ 20
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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
9.2 years ago svlachavas ▴ 830
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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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991
views
SAM : warning messages problem
siggenes siggenes
updated 20.1 years ago by 65k • written 20.1 years ago by ▴ 90
0
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3
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969
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
views
Confusion for choosing package for microarray data analysis
Microarray limma siggenes marray Microarray limma siggenes marray
updated 20.1 years ago by ▴ 140 • written 20.1 years ago by ▴ 60
0
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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
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 16.0 years ago by ▴ 900 • written 16.0 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 17.0 years ago by ★ 7.4k • written 17.0 years ago by ▴ 80
0
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3
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1.0k
views
about siggenes
siggenes siggenes
updated 19.6 years ago by ▴ 900 • written 19.6 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 11.2 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
votes
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
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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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
votes
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
replies
2.7k
views
Could you help me
siggenes siggenes
updated 19.2 years ago by ▴ 900 • written 19.2 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 20.1 years ago by 65k • written 20.1 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 12.8 years ago by ▴ 900 • written 12.8 years ago by ★ 1.5k
0
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1
reply
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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1
reply
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
votes
1
reply
1.1k
views
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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1
reply
1.2k
views
siggenes parameters
siggenes siggenes
12.8 years ago Assa Yeroslaviz ★ 1.5k
0
votes
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
votes
1
reply
942
views
Error message from running SAM for one-class case(siggenes)
siggenes siggenes
19.3 years ago Fangxin Hong ▴ 810
0
votes
1
reply
992
views
annotation problem with hgu133plus2
Annotation GO hgu133plus2 cdf annotate affy siggenes annaffy Annotation GO hgu133plus2
18.9 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
votes
1
reply
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
729
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
838
views
siggenes error with rma & wilcoxon test
siggenes siggenes
updated 18.5 years ago by ▴ 900 • written 18.5 years ago by ▴ 250
0
votes
1
reply
761
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
987
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 15.4 years ago by ▴ 400 • written 15.4 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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Answer: Dominance Index for Shotgun Metagenomics Data by Leo Lahti ▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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