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glmfit
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EdgeR - How to set up the design matrix for a multifactorial experimental design with interactions?
edger
edger main and interaction effects
glmfit
updated 5.3 years ago by
Aaron Lun
★ 28k • written 5.3 years ago by
D
• 0
3
votes
1
reply
4.7k
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edgeR: exactTest, glmFIt or glmQLFit approach?
edger
rnaseq
glm
glmfit
updated 7.2 years ago by
Aaron Lun
★ 28k • written 7.2 years ago by
alessia.donato
• 0
0
votes
3
replies
1.7k
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Standard errors of fitted values from glmFit in edgeR
edger
standard error
glmfit
7.2 years ago
david.hughes
• 0
7
votes
5
replies
3.2k
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edgeR effects of design on testing main effects and interactions
edger
glmfit
glmlrt()
updated 7.9 years ago by
Aaron Lun
★ 28k • written 7.9 years ago by
cadeans
• 0
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Answer: shinyMethyl - saving the file
by
Guillaume Devailly
▴ 60
You can probably save individual plots by right-clicking on them an save individual images. Maybe printing the page as a pdf will also work…
Answer: Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
by
Michael Love
40k
Did you manually calculate RPMs? Try `fpm(dds)` for comparison, as this also uses DESeq2 median ratio scaling.
Comment: collapseReplicates error after tximeta
by
Michael Love
40k
A note: I've now changed collapseReplicates() to output a loud warning when it is run on a DESeqDataSet (SummarizedExperiment) with more th…
Comment: Suggested package missing from Development version of Bioconductor
by
shepherl
3.5k
Have you tried reaching out to the maintainers? If they do not fix the package it will remain unavailable and cause ERROR in your package.…
Answer: Batch effect adjust in model matrix
by
ATpoint
★ 3.4k
Each sample is a different day, that is called "nested", so there is nothing you can do here. Next time do a better experimental design, he…
Votes
Comment: Batch correction and repeated measures
batch effect : comBat or blocking in limma ?
Batch correction and repeated measures
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
Comment: Phenotype effect - building a contrast matrix - grouping vs interaction
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