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treat
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12
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Appropriate use of the function treat of the limma package
limma
treat
microarray
bioconductor
9.1 years ago
svlachavas
▴ 830
5
votes
10
replies
4.3k
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Interpretation of results for treat & topTreat functions from limma regarding microarray abalysis
limma
treat
topTreat
microarray
updated 7.9 years ago by
Gordon Smyth
50k • written 7.9 years ago by
svlachavas
▴ 830
1
vote
2
replies
2.2k
views
Appropriate use of Limma Treat function
limma
treat
updated 7.1 years ago by
Aaron Lun
★ 28k • written 7.1 years ago by
danielle.newby
• 0
1
vote
2
replies
1.2k
views
TREAT function - how to interpret the result
limma
treat
updated 6.6 years ago by
Gordon Smyth
50k • written 6.6 years ago by
Sanches
• 0
4 results • Page
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Comment: Reproducibility issue with scran together with lapply and BiocParallel
by
ATpoint
★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel
by
Aaron Lun
★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio
by
Aaliya
• 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Votes
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A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
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