Showing : maanova • reset
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Statistical power of limma vs mixed model approach to analyze microarray and differentialproteomics/peptidomics experiments and Poisson/binomial mixe…
limma maanova rnaseq
11.4 years ago • updated 3.0 years ago Gordon Smyth 52k
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multicore version of maanova
maanova maanova
11.2 years ago Guest User ★ 13k
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R / Maanova: contrasts for interaction in model with 2 fixed factors
maanova maanova
12.6 years ago V. Oostra ▴ 30
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Cross-comparison of independent intensities from different experiments (genepix) (sorry I don\'t know how to describe the problem better)
limma maanova limma maanova
12.8 years ago James W. MacDonald 67k
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CRAN packages maintained by you
hexbin gpls RBGL impute Icens hopach maanova RLMM CORREP cycle hexbin gpls RBGL Icens
updated 13.1 years ago by ▴ 430 • written 13.1 years ago by ▴ 10
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R/BioC/Mac keeps going and going
maanova maanova
14.6 years ago Loren Engrav ★ 1.0k
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[MAANOVA] Contrasts for interaction levels - possible?
maanova maanova
14.7 years ago boczniak767 ▴ 740
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1.7k
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[MAANOVA] Warnings in fitmaanova & information request
maanova oligo maanova oligo
14.7 years ago boczniak767 ▴ 740
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Loop design - biological, technical replication
limma maanova limma maanova
14.7 years ago boczniak767 ▴ 740
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1.3k
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manova contrast.matrix
maanova maanova
15.0 years ago David ▴ 860
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875
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To bioinformatics and maanova expert
PROcess maanova PROcess maanova
15.4 years ago Loren Engrav ★ 1.0k
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Ignore maanova warning messages?
maanova maanova
15.4 years ago Loren Engrav ★ 1.0k
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1.2k
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Warning serious?
maanova maanova
updated 15.4 years ago by ▴ 130 • written 15.4 years ago by ★ 1.0k
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902
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What does maanova contrast?
maanova maanova
15.4 years ago Loren Engrav ★ 1.0k
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Filter before? Filter after? With maanova
Regression probe maanova Regression probe maanova
updated 15.4 years ago by ★ 5.5k • written 15.4 years ago by ★ 1.0k
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Commands with maanova
Regression maanova Regression maanova
15.4 years ago Loren Engrav ★ 1.0k
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Random effects and variance components (was: Yet another nested design in limma)
affy limma siggenes factDesign maanova affy limma siggenes factDesign maanova
updated 15.5 years ago by 67k • written 15.5 years ago by ▴ 320
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Yet another nested design in limma
affy limma siggenes factDesign maanova affy limma siggenes factDesign maanova
updated 15.6 years ago by ▴ 320 • written 15.6 years ago by 52k
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Yet another nested design in limma
affy limma siggenes factDesign maanova affy limma siggenes factDesign maanova
15.6 years ago Paolo Innocenti ▴ 320
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1.2k
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No degree of freedom in maanova
maanova maanova
15.7 years ago Marcelo Laia ▴ 450
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error with get(getOption("device")) in maanova with R 2.8.0
GO maanova GO maanova
16.1 years ago Wolfgang Huber ★ 13k
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1.3k
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error with get(getOption("device")) in maanova with R 2.8.0
Kidney maanova Kidney maanova
updated 16.1 years ago by ★ 13k • written 16.1 years ago by ▴ 20
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Does old workspace work?
Regression probe gcrma PROcess maanova Regression probe gcrma PROcess maanova
updated 16.1 years ago by ★ 6.5k • written 16.1 years ago by ★ 1.0k
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Maanova & createdata
Regression maanova Regression maanova
updated 16.1 years ago by ▴ 450 • written 16.1 years ago by ★ 1.0k
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F tests of covariates in maanova
maanova maanova
16.2 years ago Kristen K Dang ▴ 50
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1.5k
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GO over representation analysis
Annotation Pathways GO Organism db0 AnnBuilder PROcess maanova AnnotationDbi Annotation
updated 16.2 years ago by ▴ 220 • written 16.3 years ago by ★ 7.2k
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9
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1.9k
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GO over representation analysis
Annotation GO maanova Annotation GO maanova
updated 16.3 years ago by ★ 7.2k • written 16.3 years ago by ▴ 310
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How to extract log ratios from two color arrays
GO hgu133a maanova GO hgu133a maanova
16.3 years ago Heike Pospisil ▴ 310
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Microarray analysis question
Microarray Normalization affy limma convert maanova Microarray Normalization affy limma
16.5 years ago Naomi Altman ★ 6.0k
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MAANOVA - how to collapse replicate spots
Genetics maanova Genetics maanova
updated 16.6 years ago by ▴ 450 • written 16.6 years ago by ▴ 110
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[SOLVED] Factorial experiment: No degree of freedom in maanova
maanova maanova
16.8 years ago Marcelo Laia ▴ 450
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3
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1.2k
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Factorial experiment: No degree of freedom in maanova
maanova maanova
updated 16.8 years ago by ▴ 450 • written 16.8 years ago by ★ 6.0k
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858
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Factorial experiment: No degree of freedom in maanova
maanova maanova
16.8 years ago Marcelo Laia ▴ 450
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902
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2 conditions time series with different number of sample at each time point
TimeCourse limma timecourse maanova TimeCourse limma timecourse maanova
16.9 years ago Naomi Altman ★ 6.0k
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1.1k
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error in maanova matest() with affymetrix
cdf affy maanova affyio cdf affy maanova affyio
updated 17.3 years ago by 67k • written 17.3 years ago by ▴ 510
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Needed help on maanova fitmaanova function
affy vsn limma maanova affyio affy vsn limma maanova affyio
17.3 years ago Marcelo Laia ▴ 450
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MAANOVA help
maanova maanova
17.4 years ago Alessandro Fazio ▴ 70
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971
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Options for spatial normalization?
Normalization maanova Normalization maanova
updated 17.7 years ago by ▴ 80 • written 17.7 years ago by ▴ 30
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limma vs. maanova for expirement with both contrasts and continuous variables
limma maanova BAC limma maanova BAC
17.9 years ago Gordon Smyth 52k
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maanova: missing observations in cov/cor
maanova maanova
18.3 years ago Matthew Vaughn ▴ 30
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4
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1.6k
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valcano plot x-values
maanova maanova
updated 18.7 years ago by 67k • written 18.7 years ago by ▴ 220
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1.7k
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adjPval and qvalue
qvalue maanova qvalue maanova
updated 18.7 years ago by 67k • written 18.7 years ago by ▴ 220
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1
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987
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diagnostics
Genetics limma maanova Genetics limma maanova
18.8 years ago alex lam RI ▴ 310
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1.3k
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affymetrix in maanova, code
qvalue maanova qvalue maanova
18.9 years ago Morten ▴ 300
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4
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1.2k
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Using MAANOVA functions
Microarray maanova Microarray maanova
updated 19.0 years ago by ▴ 20 • written 19.0 years ago by ▴ 10
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R/maanova
Microarray affy limma maanova Microarray affy limma maanova
19.0 years ago Gary Churchill ▴ 10
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3
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1.6k
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Limma vs Maanova, and use of covariates
limma maanova limma maanova
19.0 years ago Ingunn Berget ▴ 150
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1
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1.4k
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limma(B) and maanova(La.svd) questions
limma maanova limma maanova
19.1 years ago Aurélie Laugraud ▴ 20
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834
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maanova error
maanova maanova
19.2 years ago Georg Otto ▴ 510
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865
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limma_design_matrix.
maanova maanova
20.4 years ago Gordon Smyth 52k
50 results • Page 1 of 1
Recent ...
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Comment: What type of counts data to import for performing Isoform analysis in edgeR by mohammedtoufiq91 ▴ 10
@gordonsmyth I am exploring workflows for differential transcript expression analysis and have been using the nfcore rnasplice pipeline, w…
Answer: What type of counts data to import for performing Isoform analysis in edgeR by Gordon Smyth 52k
I haven't used nf-core but, from browsing through their documentation, they didn't seem to have any pipeline for differential transcript ex…
Comment: What type of counts data to import for performing Isoform analysis in edgeR by Gordon Smyth 52k
The poster needs to run Salmon with `--numGibbsSamples=50`. I suspect that nf-core just won't do that, so Salmon needs to be run directly.
Comment: What type of counts data to import for performing Isoform analysis in edgeR by ATpoint ★ 4.6k
Probably nf-core did not run with bootstrap/gibbs replicates. Check the code. See salmon docs on how to turn that on.
Comment: What type of counts data to import for performing Isoform analysis in edgeR by mohammedtoufiq91 ▴ 10
@atpoint Thank you. I did wanted to try using the `quant.sf` files from the `salmon` run by referring edgeR user guide example `4.6 Differe…
Votes
Answer: What type of counts data to import for performing Isoform analysis in edgeR
Transcript-level differential expression using DESeq2
Comment: What type of counts data to import for performing Isoform analysis in edgeR
Answer: What type of counts data to import for performing Isoform analysis in edgeR
Comment: ANOVA like approach of edgeR
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