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ma-plot
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Weird MAplot with DEGs lying along the diagonals
limma
Microarray
AgilentChip
MA-plot
Normalization
4.0 years ago • updated 3.9 years ago
FedeXandeR
• 0
1
vote
4
replies
1.3k
views
How to spot genes/transcripts in a MA-plot
ma-plot
deseq2
updated 6.5 years ago by
Aaron Lun
★ 28k • written 6.5 years ago by
vincentpailler
• 0
0
votes
0
replies
762
views
Do my MA-plots look fine?
ma-plot
6.5 years ago
vincentpailler
• 0
2
votes
2
replies
2.9k
views
[DESeq2] Odd patterns in MA plot
deseq2
MA-plot
updated 6.9 years ago by
Ryan C. Thompson
★ 7.9k • written 6.9 years ago by
Mike
▴ 10
4 results • Page
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Comment: Use of limma R package with targeted proteomics for DE analysis
by
svlachavas
▴ 840
Dear Gordon, thanks a million for your reply (just saw it, did not get any notification through email) !! Regarding the log2 transformation…
Answer: cameraPR() non directional test
by
Gordon Smyth
52k
Yes, you can still do non-directional tests using cameraPR(), but it's not quite as easy as it was using the original camera() function as …
Answer: WGCNA with paired samples
by
Ivo
• 0
You can use batch correction on the person ID and then continue WGCNA as usual using the corrected matrix. You can use e.g. sva::ComBat or …
Answer: Plot title for PCA in DESeq2
by
ATpoint
★ 4.7k
The function uses ggplot2, so you need `+ ggtitle('title')`. Please take a ggplot2 tutorial for details.
Comment: DESeq2 It is correct to use interaction term for patient variability?
by
Bradley
• 0
I apologize, but I am still perplexed. I need to know the exact type of replication. Do we have many samples taken from the same tumor? You…
Votes
Answer: limma::voom vs edgeR::voomLmFit - when to use?
Answer: limma::voom vs edgeR::voomLmFit - when to use?
Comment: limma::voom vs edgeR::voomLmFit - when to use?
Comment: limma::voom vs edgeR::voomLmFit - when to use?
Answer: Plot title for PCA in DESeq2
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