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 9.6 years ago by 65k • written 9.6 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 14.0 years ago by ★ 13k • written 14.0 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 19.6 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
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
9.2 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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992
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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973
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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 20.1 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 17.1 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 19.6 years ago by ▴ 900 • written 19.6 years ago by ▴ 20
0
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3
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1.9k
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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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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
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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
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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 19.2 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
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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
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 17.5 years ago by ▴ 900 • written 17.5 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
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1
reply
1.1k
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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
12.8 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
943
views
Error message from running SAM for one-class case(siggenes)
siggenes siggenes
19.3 years ago Fangxin Hong ▴ 810
0
votes
1
reply
994
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
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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
731
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
840
views
siggenes error with rma & wilcoxon test
siggenes siggenes
updated 18.5 years ago by ▴ 900 • written 18.6 years ago by ▴ 250
0
votes
1
reply
762
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 15.5 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
Recent ...
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Answer: log2FoldChange value is way too different when compared with counts(dds) by Michael Love 41k
This has been asked before, but with a multi factor design, the LFC for coefficient X adjust for the others, in a way that is often hard to…
Answer: Get genomic coordinates of CpGs sites (chromosomes, genomic position) by James W. MacDonald 65k
You don't say what array that is, so I will guess. ``` > library(IlluminaHumanMethylationEPICanno.ilm10b4.hg19) > Locations DataFrame…
Answer: SGSeq: moving toward diffex from SGSeq analysis by Leonard Goldstein ▴ 200
`vid` and `eid` are unique identifiers for splice variants and splicing events respectively. They are analogous to exon bin and gene identi…
Comment: Help with error using camera() in limma by Chris • 0
Thanks James! I fixed the error. I try gene symbol instead of entrez and it worked.
Comment: limma for gene expression analysis with big and unbalanced sample size by XW • 0
Could you explain more about the comment "there are no problems with using limma for unbalanced data sets" ? thanks.
Votes
SPIA plotP giving error
Answer: Fold change calculation in Diffbind vs. DESEQ2?
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
C: Extremely big genes in annotation TxDb packages
Make custom Txdb class objects from Txdb
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