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multtest
•
reset
0
votes
0
replies
565
views
Correcting for multiple comparisons in permutation procedure using multtest
multtest
ss.maxT
ss.minP
sd.maxT
4.0 years ago
john.gordon.yellow
• 0
0
votes
1
reply
870
views
Trouble with multtest
mt.teststat
multtest
6.6 years ago
dutzr14
• 0
0
votes
1
reply
1.2k
views
Cannot load library multtest; package or namespace load failed
multtest
7.5 years ago
Guido Hooiveld
★ 3.9k
1
vote
1
reply
1.2k
views
Not getting Adjusted p-values from multtest package
multtest
methylation
adjusted pvalue
updated 8.5 years ago by
kpollard
▴ 110 • written 8.5 years ago by
elhananby
▴ 10
4
votes
2
replies
5.9k
views
Adjust p-values of a matrix of p-values
multtest
updated 9.5 years ago by
Gordon Smyth
50k • written 9.5 years ago by
Jon Bråte
▴ 250
0
votes
2
replies
1.2k
views
About correlation tests between pairs of genes
multtest
updated 9.5 years ago by
Simon Anders
★ 3.7k • written 9.5 years ago by
Jon Bråte
▴ 250
1
vote
0
replies
1.8k
views
DE analysis of PCR array [was: dataset dim for siggenes]
qPCR
Normalization
multtest
limma
siggenes
9.7 years ago • updated 7.3 years ago
Gordon Smyth
50k
0
votes
1
reply
1.4k
views
prefiltering genelist before LIMMA & cut-off paramter for getting DEGs from topT object.
multtest
multtest
updated 10.4 years ago by
Steve Lianoglou
★ 13k • written 10.4 years ago by
Guest User
★ 13k
0
votes
0
replies
1.7k
views
Fwd: (adj.p.value & log2FC) or (B.value & log2FC)
multtest
limma
multtest
limma
10.4 years ago
debatosh das
▴ 10
0
votes
0
replies
1.0k
views
question about wilcoxon sign rank in multtest package
multtest
multtest
11.7 years ago
Islam Amin
▴ 10
0
votes
0
replies
1.1k
views
converting intensity values to log ratios?
multtest
limma
siggenes
convert
multtest
limma
siggenes
convert
12.3 years ago
James W. MacDonald
65k
0
votes
1
reply
902
views
Difference between Multtest and SAM
multtest
multtest
updated 13.3 years ago by
Sean Davis
21k • written 13.3 years ago by
Peevi Ijkl
▴ 170
0
votes
3
replies
994
views
class label
Normalization
multtest
Normalization
multtest
updated 13.4 years ago by
Martin Morgan
25k • written 13.4 years ago by
Peevi Ijkl
▴ 170
0
votes
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
Martin Morgan
25k • written 13.4 years ago by
Jillian Rowe
▴ 20
0
votes
1
reply
1.5k
views
problems : getting error : Error in .checkKeys(value, Lkeys(x), x@ifnotfound) : value for "GO:0010817" not found
multtest
GOstats
biomaRt
multtest
GOstats
biomaRt
updated 14.3 years ago by
James W. MacDonald
65k • written 14.3 years ago by
Andreia Fonseca
▴ 810
0
votes
1
reply
1.0k
views
Question on the paired ttest in multtest package
multtest
multtest
updated 14.8 years ago by
James W. MacDonald
65k • written 14.8 years ago by
Anqi
▴ 40
0
votes
0
replies
1.2k
views
multtest: how to adjust multiple contrasts in a single run?
moe430a
multtest
affy
limma
moe430a
multtest
affy
limma
14.9 years ago
Guido Hooiveld
★ 3.9k
0
votes
3
replies
3.4k
views
problem updating packages importing the package "MASS"
multtest
multtest
updated 15.0 years ago by
Sean Davis
21k • written 15.0 years ago by
Mark W Kimpel
▴ 830
0
votes
0
replies
865
views
P-values returned from siggenes's sam() function
multtest
multtest
15.0 years ago
Michal Blazejczyk
▴ 320
0
votes
1
reply
1.4k
views
Limma- Filtering After Statistical Analysis
genefilter
multtest
limma
genefilter
multtest
limma
updated 15.3 years ago by
Gordon Smyth
50k • written 15.3 years ago by
Sally
▴ 250
0
votes
0
replies
985
views
Help for ANOVA test
multtest
limma
multtest
limma
15.3 years ago
John Antonydas Gaspar
▴ 130
0
votes
2
replies
1.5k
views
multtest different seed
multtest
multtest
15.6 years ago
Stefano Moretti
▴ 20
0
votes
2
replies
1.4k
views
'Factorial Design' package question
Survival
cdf
multtest
affy
factDesign
biomaRt
Survival
cdf
multtest
affy
factDesign
15.9 years ago
Glazko, Galina
▴ 350
0
votes
3
replies
1.2k
views
Webbioc error exprSet vs expressionSet
Preprocessing
multtest
webbioc
Preprocessing
multtest
webbioc
16.1 years ago
Balasubramanian Ganesan
▴ 70
0
votes
0
replies
994
views
Extracting expressions after a multtest procedure (part2)
Cancer
multtest
Cancer
multtest
16.2 years ago
JUAN MIGUEL MARIN DIAZARAQUE
▴ 70
0
votes
3
replies
1.1k
views
Extracting expressions after a multtest procedure (part 2)
multtest
multtest
updated 16.2 years ago by
Sean Davis
21k • written 16.2 years ago by
JUAN MIGUEL MARIN DIAZARAQUE
▴ 70
0
votes
0
replies
1.1k
views
Extracting expressions after a multtest procedure
multtest
multtest
16.2 years ago
JUAN MIGUEL MARIN DIAZARAQUE
▴ 70
0
votes
0
replies
1.3k
views
multtest MTP raw P values = 0
multtest
multtest
16.2 years ago
Timur Shtatland
▴ 30
0
votes
0
replies
1.2k
views
multtest MTP raw P values = 0
multtest
multtest
16.2 years ago
Timur Shtatland
▴ 30
0
votes
0
replies
788
views
p-value output from MTP (multtest) into scientific notations
multtest
multtest
16.4 years ago
Boel Brynedal
▴ 200
0
votes
0
replies
1.1k
views
MTP error
GO
Survival
multtest
affy
affydata
annaffy
affyPLM
affyio
GO
Survival
multtest
affy
16.5 years ago
Boel Brynedal
▴ 200
0
votes
1
reply
781
views
Limma: eBayes makes p-values larger
Cancer
multtest
limma
Cancer
multtest
limma
updated 16.5 years ago by
James W. MacDonald
65k • written 16.5 years ago by
Daniel Brewer
★ 1.9k
0
votes
0
replies
1.8k
views
how to convert a AffyBatch into ExpressionSet object ?
Annotation
GO
Survival
ExperimentData
cdf
DynDoc
genefilter
geneplotter
multtest
affy
GO
16.7 years ago
Min Wook Kim
▴ 20
0
votes
6
replies
3.4k
views
how to convert a AffyBatch into ExpressionSet object ?
Annotation
GO
Survival
ExperimentData
cdf
DynDoc
genefilter
geneplotter
multtest
affy
GO
updated 16.7 years ago by
Weiyin Zhou
▴ 220 • written 16.7 years ago by
Jenny Drnevich
★ 2.2k
0
votes
1
reply
1.2k
views
Imputation problem in aCGH
aCGH
Biobase
multtest
impute
aCGH
aCGH
Biobase
multtest
impute
aCGH
16.8 years ago
Benjamin Otto
▴ 830
0
votes
1
reply
1.3k
views
snapCGH; export results of summarize.clones() function from aCGH
aCGH
Survival
Cancer
Breast
Biobase
annotate
genefilter
geneplotter
multtest
limma
aCGH
16.9 years ago
Steven McKinney
▴ 310
0
votes
2
replies
1.1k
views
help for siggene installation
Biobase
multtest
Biobase
multtest
updated 17.0 years ago by
Seth Falcon
★ 7.4k • written 17.0 years ago by
Ruma Sanyal
▴ 60
0
votes
3
replies
2.0k
views
hyperGTest, KEGG
Annotation
Pathways
multtest
siggenes
RBGL
GOstats
Annotation
Pathways
multtest
siggenes
updated 17.1 years ago by
Seth Falcon
★ 7.4k • written 17.1 years ago by
ivan.borozan@utoronto.ca
▴ 80
0
votes
3
replies
1.3k
views
webbioc chicken
Microarray
cdf
probe
multtest
affy
webbioc
Microarray
cdf
probe
multtest
affy
webbioc
updated 17.2 years ago by
Nianhua Li
▴ 870 • written 17.2 years ago by
jane janes
▴ 20
0
votes
3
replies
1.2k
views
GOstats hyperGTest question
Biobase
annotate
genefilter
multtest
graph
Biobase
annotate
genefilter
multtest
graph
updated 17.3 years ago by
Seth Falcon
★ 7.4k • written 17.3 years ago by
ivan.borozan@utoronto.ca
▴ 80
0
votes
2
replies
1.2k
views
imputing missing data for 70mer array platform, need advice
aCGH
CGH
multtest
impute
aCGH
oligo
aCGH
CGH
multtest
impute
aCGH
oligo
updated 17.3 years ago by
Sean Davis
21k • written 17.3 years ago by
Betty Gilbert
▴ 50
0
votes
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
Holger Schwender
▴ 900 • written 17.5 years ago by
Martin Morgan
25k
0
votes
5
replies
1.5k
views
error coercing an exprSet to ExpressionSet
GO
cdf
Biobase
annotate
multtest
affy
limma
RBGL
GOstats
Category
affycoretools
GO
cdf
updated 17.5 years ago by
Seth Falcon
★ 7.4k • written 17.5 years ago by
Kimpel, Mark W
▴ 890
0
votes
0
replies
1.0k
views
help with RankProd plaase
GO
Survival
cdf
genefilter
multtest
affy
limma
RankProd
Category
affycoretools
GO
cdf
17.5 years ago
Kimpel, Mark W
▴ 890
0
votes
0
replies
1.2k
views
problems with Affy vignette and affybatch objects
GO
Survival
cdf
Biobase
annotate
genefilter
multtest
affy
affydata
graph
limma
gcrma
17.5 years ago
Martin Morgan
25k
0
votes
4
replies
1.2k
views
problems with Affy vignette and affybatch objects
GO
Survival
cdf
Biobase
annotate
genefilter
multtest
reposTools
affy
affydata
graph
GO
updated 17.5 years ago by
Martin Morgan
25k • written 17.5 years ago by
Jenny Drnevich
★ 2.2k
0
votes
0
replies
662
views
sensitivity of maxT correction
multtest
multtest
17.6 years ago
A S
▴ 10
0
votes
3
replies
2.0k
views
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 17.6 years ago by
James W. MacDonald
65k • written 17.6 years ago by
Jordi Altirriba Gutiérrez
▴ 350
0
votes
2
replies
1.0k
views
error with GOHyperG
drosophila2
cdf
Biobase
annotate
genefilter
multtest
RBGL
GOstats
drosophila2
cdf
RBGL
updated 17.7 years ago by
Seth Falcon
★ 7.4k • written 17.7 years ago by
Tony Long
▴ 10
0
votes
1
reply
1.3k
views
[R] problem loading affycoretools - solved!
Biobase
Ruuid
genefilter
multtest
graph
limma
gcrma
matchprobes
affyPLM
RBGL
simpleaffy
updated 17.8 years ago by
Seth Falcon
★ 7.4k • written 17.8 years ago by
Jenny Drnevich
★ 2.2k
50 results • Page
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Replies
Comment: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
by
Dylan.Sheerin
• 0
Thank you very much, Gordon. I'll give voomLmFit a go! And for comparisons between the cohorts I presume duplicateCorrelation with standar…
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
by
Gordon Smyth
50k
Including subjectID in the design matrix always accounts for unbalanced sampling and patient variation but subjects with incomplete records…
Comment: Log-cpm values from limma
by
Gordon Smyth
50k
No, it does not mean that. `voom()` uses the design matrix, including the W covariates, to compute precision weights but not to adjust the …
Comment: Extremely small p-values using Limma for proteomic data
by
Abbey
• 0
This is the code. The only part I changed was adding the contrasts.fit as you suggested. Thanks for taking a look! ``` # Load necessary …
Comment: Extremely small p-values using Limma for proteomic data
by
James W. MacDonald
65k
Probably. I would not expect such large fold changes. But without seeing your code, who knows?
Votes
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
Answer: Extremely small p-values using Limma for proteomic data
Bioconductor 3.19 is Released!
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
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