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
12.5 years ago • updated 4.0 years ago Gordon Smyth 53k
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multicore version of maanova
maanova maanova
12.2 years ago Guest User ★ 13k
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R / Maanova: contrasts for interaction in model with 2 fixed factors
maanova maanova
13.6 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
13.9 years ago James W. MacDonald 68k
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CRAN packages maintained by you
hexbin gpls RBGL impute Icens hopach maanova RLMM CORREP cycle hexbin gpls RBGL Icens
updated 14.1 years ago by ▴ 430 • written 14.1 years ago by ▴ 10
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R/BioC/Mac keeps going and going
maanova maanova
15.7 years ago Loren Engrav ★ 1.0k
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[MAANOVA] Contrasts for interaction levels - possible?
maanova maanova
15.7 years ago boczniak767 ▴ 740
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[MAANOVA] Warnings in fitmaanova & information request
maanova oligo maanova oligo
15.8 years ago boczniak767 ▴ 740
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Loop design - biological, technical replication
limma maanova limma maanova
15.8 years ago boczniak767 ▴ 740
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manova contrast.matrix
maanova maanova
16.0 years ago David ▴ 860
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999
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To bioinformatics and maanova expert
PROcess maanova PROcess maanova
16.4 years ago Loren Engrav ★ 1.0k
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Ignore maanova warning messages?
maanova maanova
16.4 years ago Loren Engrav ★ 1.0k
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3
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1.4k
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Warning serious?
maanova maanova
updated 16.4 years ago by ▴ 130 • written 16.4 years ago by ★ 1.0k
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What does maanova contrast?
maanova maanova
16.4 years ago Loren Engrav ★ 1.0k
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Filter before? Filter after? With maanova
Regression probe maanova Regression probe maanova
updated 16.4 years ago by ★ 5.5k • written 16.4 years ago by ★ 1.0k
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Commands with maanova
Regression maanova Regression maanova
16.4 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 16.5 years ago by 68k • written 16.5 years ago by ▴ 320
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3.2k
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Yet another nested design in limma
affy limma siggenes factDesign maanova affy limma siggenes factDesign maanova
updated 16.6 years ago by ▴ 320 • written 16.6 years ago by 53k
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Yet another nested design in limma
affy limma siggenes factDesign maanova affy limma siggenes factDesign maanova
16.6 years ago Paolo Innocenti ▴ 320
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1.3k
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No degree of freedom in maanova
maanova maanova
16.8 years ago • updated 16.7 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
17.1 years ago Wolfgang Huber ★ 13k
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1.5k
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error with get(getOption("device")) in maanova with R 2.8.0
Kidney maanova Kidney maanova
updated 17.1 years ago by ★ 13k • written 17.1 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 17.1 years ago by ★ 6.5k • written 17.1 years ago by ★ 1.0k
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2
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Maanova & createdata
Regression maanova Regression maanova
updated 17.1 years ago by ▴ 450 • written 17.1 years ago by ★ 1.0k
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F tests of covariates in maanova
maanova maanova
17.3 years ago Kristen K Dang ▴ 50
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2
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1.7k
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GO over representation analysis
Annotation Pathways GO Organism db0 AnnBuilder PROcess maanova AnnotationDbi Annotation
updated 17.3 years ago by ▴ 220 • written 17.3 years ago by ★ 7.2k
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GO over representation analysis
Annotation GO maanova Annotation GO maanova
updated 17.3 years ago by ★ 7.2k • written 17.3 years ago by ▴ 310
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1
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1.1k
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How to extract log ratios from two color arrays
GO hgu133a maanova GO hgu133a maanova
17.3 years ago Heike Pospisil ▴ 310
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Microarray analysis question
Microarray Normalization affy limma convert maanova Microarray Normalization affy limma
17.5 years ago Naomi Altman ★ 6.0k
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MAANOVA - how to collapse replicate spots
Genetics maanova Genetics maanova
updated 17.6 years ago by ▴ 450 • written 17.6 years ago by ▴ 110
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[SOLVED] Factorial experiment: No degree of freedom in maanova
maanova maanova
17.8 years ago Marcelo Laia ▴ 450
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3
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1.5k
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Factorial experiment: No degree of freedom in maanova
maanova maanova
updated 17.8 years ago by ▴ 450 • written 17.8 years ago by ★ 6.0k
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972
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Factorial experiment: No degree of freedom in maanova
maanova maanova
17.8 years ago Marcelo Laia ▴ 450
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0
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1.0k
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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
17.9 years ago Naomi Altman ★ 6.0k
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error in maanova matest() with affymetrix
cdf affy maanova affyio cdf affy maanova affyio
updated 18.3 years ago by 68k • written 18.3 years ago by ▴ 510
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Needed help on maanova fitmaanova function
affy vsn limma maanova affyio affy vsn limma maanova affyio
18.4 years ago Marcelo Laia ▴ 450
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844
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MAANOVA help
maanova maanova
18.4 years ago Alessandro Fazio ▴ 70
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1.1k
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Options for spatial normalization?
Normalization maanova Normalization maanova
updated 18.8 years ago by ▴ 80 • written 18.8 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
18.9 years ago Gordon Smyth 53k
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992
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maanova: missing observations in cov/cor
maanova maanova
19.3 years ago Matthew Vaughn ▴ 30
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4
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1.8k
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valcano plot x-values
maanova maanova
updated 19.7 years ago by 68k • written 19.7 years ago by ▴ 220
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1.9k
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adjPval and qvalue
qvalue maanova qvalue maanova
updated 19.7 years ago by 68k • written 19.7 years ago by ▴ 220
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1
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1.2k
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diagnostics
Genetics limma maanova Genetics limma maanova
19.9 years ago • updated 19.8 years ago alex lam RI ▴ 310
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1.5k
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affymetrix in maanova, code
qvalue maanova qvalue maanova
19.9 years ago Morten ▴ 300
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4
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1.4k
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Using MAANOVA functions
Microarray maanova Microarray maanova
updated 20.0 years ago by ▴ 20 • written 20.0 years ago by ▴ 10
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R/maanova
Microarray affy limma maanova Microarray affy limma maanova
20.0 years ago Gary Churchill ▴ 10
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3
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1.8k
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Limma vs Maanova, and use of covariates
limma maanova limma maanova
20.0 years ago Ingunn Berget ▴ 150
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1
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1.5k
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limma(B) and maanova(La.svd) questions
limma maanova limma maanova
20.2 years ago Aurélie Laugraud ▴ 20
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928
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maanova error
maanova maanova
20.2 years ago Georg Otto ▴ 510
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0
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956
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limma_design_matrix.
maanova maanova
21.5 years ago Gordon Smyth 53k
55 results • Page 1 of 2
Recent ...
Replies
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Awards • All
Popular Question to James W. MacDonald 68k
Popular Question to Gordon Smyth 53k
Commentator to sina.nassiri ▴ 130
Popular Question to Hervé Pagès 16k
Popular Question to jared.andrews07 ▴ 30
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