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
9.6 years ago • updated 13 months ago Gordon Smyth 47k
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multicore version of maanova
maanova maanova
9.3 years ago Guest User ★ 12k
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R / Maanova: contrasts for interaction in model with 2 fixed factors
maanova maanova
10.7 years ago V. Oostra ▴ 30
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541
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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
11.0 years ago James W. MacDonald 62k
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1
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973
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CRAN packages maintained by you
hexbin gpls RBGL impute Icens hopach maanova RLMM CORREP cycle hexbin gpls RBGL Icens
updated 11.2 years ago by ▴ 430 • written 11.2 years ago by ▴ 10
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566
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R/BioC/Mac keeps going and going
maanova maanova
12.8 years ago Loren Engrav ★ 1.0k
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723
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[MAANOVA] Contrasts for interaction levels - possible?
maanova maanova
12.8 years ago Maciej Jończyk ▴ 720
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3
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1.2k
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[MAANOVA] Warnings in fitmaanova & information request
maanova oligo maanova oligo
12.9 years ago Maciej Jończyk ▴ 720
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800
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Loop design - biological, technical replication
limma maanova limma maanova
12.9 years ago Maciej Jończyk ▴ 720
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956
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manova contrast.matrix
maanova maanova
13.1 years ago David ▴ 860
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595
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To bioinformatics and maanova expert
PROcess maanova PROcess maanova
13.5 years ago Loren Engrav ★ 1.0k
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656
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Ignore maanova warning messages?
maanova maanova
13.6 years ago Loren Engrav ★ 1.0k
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3
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744
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Warning serious?
maanova maanova
updated 13.6 years ago by ▴ 130 • written 13.6 years ago by ★ 1.0k
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625
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What does maanova contrast?
maanova maanova
13.6 years ago Loren Engrav ★ 1.0k
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2
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684
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Filter before? Filter after? With maanova
Regression probe maanova Regression probe maanova
updated 13.6 years ago by ★ 5.5k • written 13.6 years ago by ★ 1.0k
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646
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Commands with maanova
Regression maanova Regression maanova
13.6 years ago Loren Engrav ★ 1.0k
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2
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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 13.7 years ago by 62k • written 13.7 years ago by ▴ 320
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2
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Yet another nested design in limma
affy limma siggenes factDesign maanova affy limma siggenes factDesign maanova
updated 13.7 years ago by ▴ 320 • written 13.7 years ago by 47k
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Yet another nested design in limma
affy limma siggenes factDesign maanova affy limma siggenes factDesign maanova
13.7 years ago Paolo Innocenti ▴ 320
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1
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821
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No degree of freedom in maanova
maanova maanova
13.9 years ago Marcelo Laia ▴ 450
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760
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error with get(getOption("device")) in maanova with R 2.8.0
GO maanova GO maanova
14.2 years ago Wolfgang Huber 13k
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1.1k
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error with get(getOption("device")) in maanova with R 2.8.0
Kidney maanova Kidney maanova
updated 14.2 years ago by 13k • written 14.2 years ago by ▴ 20
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2
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Does old workspace work?
Regression probe gcrma PROcess maanova Regression probe gcrma PROcess maanova
updated 14.2 years ago by 6.5k • written 14.2 years ago by ★ 1.0k
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2
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Maanova & createdata
Regression maanova Regression maanova
updated 14.2 years ago by ▴ 450 • written 14.2 years ago by ★ 1.0k
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801
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F tests of covariates in maanova
maanova maanova
14.4 years ago Kristen K Dang ▴ 50
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2
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987
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GO over representation analysis
Annotation Pathways GO Organism db0 AnnBuilder PROcess maanova AnnotationDbi Annotation
updated 14.4 years ago by ▴ 220 • written 14.4 years ago by ★ 7.2k
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9
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1.3k
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GO over representation analysis
Annotation GO maanova Annotation GO maanova
updated 14.4 years ago by ★ 7.2k • written 14.4 years ago by ▴ 310
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1
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707
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How to extract log ratios from two color arrays
GO hgu133a maanova GO hgu133a maanova
14.4 years ago Heike Pospisil ▴ 310
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518
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Microarray analysis question
Microarray Normalization affy limma convert maanova Microarray Normalization affy limma
14.6 years ago Naomi Altman ★ 6.0k
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1
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752
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MAANOVA - how to collapse replicate spots
Genetics maanova Genetics maanova
updated 14.8 years ago by ▴ 450 • written 14.8 years ago by ▴ 110
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[SOLVED] Factorial experiment: No degree of freedom in maanova
maanova maanova
14.9 years ago Marcelo Laia ▴ 450
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3
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799
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Factorial experiment: No degree of freedom in maanova
maanova maanova
updated 14.9 years ago by ▴ 450 • written 14.9 years ago by ★ 6.0k
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614
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Factorial experiment: No degree of freedom in maanova
maanova maanova
14.9 years ago Marcelo Laia ▴ 450
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636
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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
15.0 years ago Naomi Altman ★ 6.0k
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1
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730
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error in maanova matest() with affymetrix
cdf affy maanova affyio cdf affy maanova affyio
updated 15.4 years ago by 62k • written 15.4 years ago by ▴ 510
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1
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Needed help on maanova fitmaanova function
affy vsn limma maanova affyio affy vsn limma maanova affyio
15.5 years ago Marcelo Laia ▴ 450
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0
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506
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MAANOVA help
maanova maanova
15.5 years ago Alessandro Fazio ▴ 70
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1
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658
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Options for spatial normalization?
Normalization maanova Normalization maanova
updated 15.9 years ago by ▴ 80 • written 15.9 years ago by ▴ 30
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867
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limma vs. maanova for expirement with both contrasts and continuous variables
limma maanova BAC limma maanova BAC
16.0 years ago Gordon Smyth 47k
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629
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maanova: missing observations in cov/cor
maanova maanova
16.4 years ago Matthew Vaughn ▴ 30
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4
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1.1k
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valcano plot x-values
maanova maanova
updated 16.9 years ago by 62k • written 16.9 years ago by ▴ 220
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1
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1.2k
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adjPval and qvalue
qvalue maanova qvalue maanova
updated 16.9 years ago by 62k • written 16.9 years ago by ▴ 220
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1
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578
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diagnostics
Genetics limma maanova Genetics limma maanova
17.0 years ago alex lam RI ▴ 310
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965
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affymetrix in maanova, code
qvalue maanova qvalue maanova
17.1 years ago Morten ▴ 300
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4
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780
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Using MAANOVA functions
Microarray maanova Microarray maanova
updated 17.1 years ago by ▴ 20 • written 17.1 years ago by ▴ 10
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888
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R/maanova
Microarray affy limma maanova Microarray affy limma maanova
17.1 years ago Gary Churchill ▴ 10
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3
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1.0k
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Limma vs Maanova, and use of covariates
limma maanova limma maanova
17.1 years ago Ingunn Berget ▴ 150
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1
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1.1k
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limma(B) and maanova(La.svd) questions
limma maanova limma maanova
17.3 years ago Aurélie Laugraud ▴ 20
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582
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maanova error
maanova maanova
17.4 years ago Georg Otto ▴ 510
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0
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613
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limma_design_matrix.
maanova maanova
18.6 years ago Gordon Smyth 47k
50 results • Page 1 of 1
Recent ...
Replies
Comment: transcript name mapping between human and mouse by Eric • 0
It works very well, and thanks for such a great answer! Because I use the old version gtf from GENECODE (vM12), the id version does not mat…
Comment: How to normalize long-read RNA-seq data for comparison with short-reads by Bernardo • 0
Just did that, thank you for the suggestion.
Comment: Empty ChipQC Report by Okan • 0
Hi, I have the same issue. Have you found any solution or any reason why this is happening?
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by Gordon Smyth 47k
Am I understanding correctly that you have 24 RNA-seq libraries in total, 6 from the pooled samples and 18 from regular samples with biolog…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by k.roelfs • 0
I'm sorry, I know it is kinda confusing... We have 6 pools in total: Phenotype A: T1a, T2, T1b, T1c Phenotype B: T1, T2 Each pool consist…
Votes
Answer: transcript name mapping between human and mouse
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
Volcano Plot in R
Answer: Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
Answer: Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
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