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Bioconductor Multtest
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Cross-validation with multiple control subgroups in limma
limma multtest
2 days ago • updated 1 day ago Ali Barry ▴ 40
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720
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Correcting for multiple comparisons in permutation procedure using multtest
multtest ss.maxT ss.minP sd.maxT
4.6 years ago john.gordon.yellow • 0
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989
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Trouble with multtest
mt.teststat multtest
7.2 years ago dutzr14 • 0
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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
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Cannot load library multtest; package or namespace load failed
multtest
8.1 years ago Guido Hooiveld ★ 4.1k
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mt.teststat
multtest DECIPHER multtest DECIPHER
updated 8.9 years ago by ▴ 20 • written 21.7 years ago by ▴ 220
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Not getting Adjusted p-values from multtest package
multtest methylation adjusted pvalue
updated 9.1 years ago by ▴ 110 • written 9.1 years ago by ▴ 10
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Adjust p-values of a matrix of p-values
multtest
updated 10.1 years ago by 52k • written 10.1 years ago by ▴ 260
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1.4k
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About correlation tests between pairs of genes
multtest
updated 10.1 years ago by ★ 3.8k • written 10.1 years ago by ▴ 260
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prefiltering genelist before LIMMA & cut-off paramter for getting DEGs from topT object.
multtest multtest
updated 11.1 years ago by ★ 13k • written 11.1 years ago by ★ 13k
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Fwd: (adj.p.value & log2FC) or (B.value & log2FC)
multtest limma multtest limma
11.1 years ago debatosh das ▴ 10
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question about wilcoxon sign rank in multtest package
multtest multtest
12.3 years ago Islam Amin ▴ 10
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1.2k
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converting intensity values to log ratios?
multtest limma siggenes convert multtest limma siggenes convert
12.9 years ago James W. MacDonald 67k
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1.0k
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Difference between Multtest and SAM
multtest multtest
updated 14.0 years ago by 21k • written 14.0 years ago by ▴ 170
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class label
Normalization multtest Normalization multtest
updated 14.0 years ago by 25k • written 14.0 years ago by ▴ 170
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1.9k
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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
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1.7k
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problems : getting error : Error in .checkKeys(value, Lkeys(x), x@ifnotfound) : value for "GO:0010817" not found
multtest GOstats biomaRt multtest GOstats biomaRt
updated 15.0 years ago by 67k • written 15.0 years ago by ▴ 810
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1.1k
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Question on the paired ttest in multtest package
multtest multtest
updated 15.4 years ago by 67k • written 15.4 years ago by ▴ 40
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1.4k
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multtest: how to adjust multiple contrasts in a single run?
moe430a multtest affy limma moe430a multtest affy limma
15.5 years ago Guido Hooiveld ★ 4.1k
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4.0k
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problem updating packages importing the package "MASS"
multtest multtest
updated 15.6 years ago by 21k • written 15.6 years ago by ▴ 830
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960
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P-values returned from siggenes's sam() function
multtest multtest
15.7 years ago Michal Blazejczyk ▴ 320
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1.6k
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Limma- Filtering After Statistical Analysis
genefilter multtest limma genefilter multtest limma
updated 15.9 years ago by 52k • written 15.9 years ago by ▴ 250
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Help for ANOVA test
multtest limma multtest limma
15.9 years ago John Antonydas Gaspar ▴ 130
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1.6k
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multtest different seed
multtest multtest
16.3 years ago Stefano Moretti ▴ 20
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1.5k
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'Factorial Design' package question
Survival cdf multtest affy factDesign biomaRt Survival cdf multtest affy factDesign
16.6 years ago Glazko, Galina ▴ 350
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Webbioc error exprSet vs expressionSet
Preprocessing multtest webbioc Preprocessing multtest webbioc
16.7 years ago Balasubramanian Ganesan ▴ 70
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Extracting expressions after a multtest procedure (part2)
Cancer multtest Cancer multtest
16.8 years ago JUAN MIGUEL MARIN DIAZARAQUE ▴ 70
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Extracting expressions after a multtest procedure (part 2)
multtest multtest
updated 16.8 years ago by 21k • written 16.8 years ago by ▴ 70
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1.2k
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Extracting expressions after a multtest procedure
multtest multtest
16.8 years ago JUAN MIGUEL MARIN DIAZARAQUE ▴ 70
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multtest MTP raw P values = 0
multtest multtest
16.8 years ago Timur Shtatland ▴ 30
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1.3k
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multtest MTP raw P values = 0
multtest multtest
16.8 years ago Timur Shtatland ▴ 30
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890
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p-value output from MTP (multtest) into scientific notations
multtest multtest
17.0 years ago Boel Brynedal ▴ 200
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1.2k
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MTP error
GO Survival multtest affy affydata annaffy affyPLM affyio GO Survival multtest affy
17.1 years ago Boel Brynedal ▴ 200
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907
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Limma: eBayes makes p-values larger
Cancer multtest limma Cancer multtest limma
updated 17.2 years ago by 67k • written 17.2 years ago by ★ 1.9k
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6
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3.7k
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how to convert a AffyBatch into ExpressionSet object ?
Annotation GO Survival ExperimentData cdf DynDoc genefilter geneplotter multtest affy GO
updated 17.3 years ago by ▴ 220 • written 17.4 years ago by ★ 2.2k
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how to convert a AffyBatch into ExpressionSet object ?
Annotation GO Survival ExperimentData cdf DynDoc genefilter geneplotter multtest affy GO
17.3 years ago Min Wook Kim ▴ 20
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1.4k
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Imputation problem in aCGH
aCGH Biobase multtest impute aCGH aCGH Biobase multtest impute aCGH
17.4 years ago Benjamin Otto ▴ 830
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1.4k
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snapCGH; export results of summarize.clones() function from aCGH
aCGH Survival Cancer Breast Biobase annotate genefilter geneplotter multtest limma aCGH
17.5 years ago Steven McKinney ▴ 310
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1.2k
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help for siggene installation
Biobase multtest Biobase multtest
updated 17.6 years ago by ★ 7.4k • written 17.6 years ago by ▴ 60
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3
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2.2k
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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
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3
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1.5k
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webbioc chicken
Microarray cdf probe multtest affy webbioc Microarray cdf probe multtest affy webbioc
updated 17.8 years ago by ▴ 870 • written 17.9 years ago by ▴ 20
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3
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GOstats hyperGTest question
Biobase annotate genefilter multtest graph Biobase annotate genefilter multtest graph
updated 17.9 years ago by ★ 7.4k • written 17.9 years ago by ▴ 80
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2
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1.3k
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imputing missing data for 70mer array platform, need advice
aCGH CGH multtest impute aCGH oligo aCGH CGH multtest impute aCGH oligo
updated 17.9 years ago by 21k • written 17.9 years ago by ▴ 50
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1.4k
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[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
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1.8k
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error coercing an exprSet to ExpressionSet
GO cdf Biobase annotate multtest affy limma RBGL GOstats Category affycoretools GO cdf
updated 18.1 years ago by ★ 7.4k • written 18.1 years ago by ▴ 890
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0
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1.1k
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help with RankProd plaase
GO Survival cdf genefilter multtest affy limma RankProd Category affycoretools GO cdf
18.1 years ago Kimpel, Mark W ▴ 890
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0
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1.3k
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problems with Affy vignette and affybatch objects
GO Survival cdf Biobase annotate genefilter multtest affy affydata graph limma gcrma
18.2 years ago Martin Morgan 25k
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4
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1.4k
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problems with Affy vignette and affybatch objects
GO Survival cdf Biobase annotate genefilter multtest reposTools affy affydata graph GO
updated 18.2 years ago by 25k • written 18.2 years ago by ★ 2.2k
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747
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sensitivity of maxT correction
multtest multtest
18.2 years ago A S ▴ 10
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3
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2.2k
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Situation of the legend in the plotPCA of the affycoretools library
GO Survival cdf annotate genefilter multtest affy graph limma RBGL GOstats Category GO
updated 18.2 years ago by 67k • written 18.2 years ago by ▴ 350
50 results • Page 1 of 1
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Comment: Cross-validation with multiple control subgroups in limma by Ali Barry ▴ 40
Thanks so much for taking the time here, the insights are much appreciated. I suspected I'd have to ad hoc compare results if I did repeat …
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…
Votes
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
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