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maplot
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Why is my log fold change not centered around 0 and lower?
DESeq2
MAplot
updated 14 months ago by
ATpoint
★ 4.0k • written 14 months ago by
Michael
• 0
10
votes
8
replies
2.1k
views
MA plot
MAplot
15 months ago
Nathalie
▴ 20
0
votes
3
replies
2.2k
views
Understanding MA plot distortion
DESeq2
MAplot
deseq
updated 3.1 years ago by
Michael Love
41k • written 3.1 years ago by
sp
• 0
1
vote
1
reply
770
views
LFCshrink function understanding
deseq2
MAplot
lfcshrink
updated 3.6 years ago by
Michael Love
41k • written 3.6 years ago by
evelas13
• 0
1
vote
2
replies
586
views
Label points on DESeq2 MA plot with interval list
deseq2
maplot
annotation
updated 4.4 years ago by
Michael Love
41k • written 4.4 years ago by
rbronste
▴ 60
2
votes
2
replies
2.5k
views
DiffBind's MA plots for ChIP-seq - how to properly interpret normalization from them?
diffbind
R
MAplot
Chipseq
updated 4.9 years ago by
Rory Stark
★ 5.1k • written 4.9 years ago by
melnuesch
▴ 10
0
votes
2
replies
1.3k
views
MA plot scattering pattern
deseq2
MAplot
5.4 years ago
avitalwasser
• 0
5
votes
8
replies
1.2k
views
High normalized counts on DESeq2 MAplot
deseq2
maplot
updated 5.4 years ago by
James W. MacDonald
65k • written 5.4 years ago by
rbronste
▴ 60
0
votes
4
replies
1.1k
views
DESeq2 MA plot normalisation Issue
deseq2
normalization
maplot
rnaseq
updated 5.5 years ago by
Michael Love
41k • written 5.5 years ago by
ma619
• 0
0
votes
1
reply
1.5k
views
MA plot interpretation .
MAPLOT
DESEQ2
RNASEQ
updated 6.2 years ago by
Michael Love
41k • written 6.2 years ago by
phurbusang
• 0
2
votes
1
reply
2.0k
views
Error in DESeq2 plotMA from object subset
deseq2
maplot
subset
updated 6.3 years ago by
Michael Love
41k • written 6.3 years ago by
rbronste
▴ 60
2
votes
4
replies
1.6k
views
DiffBind MA plot
diffbind
maplot
updated 6.3 years ago by
Rory Stark
★ 5.1k • written 6.3 years ago by
grundelphine
• 0
1
vote
2
replies
1.2k
views
DiffBind DESeq2 MA plot skewed
diffbind
deseq2
maplot
updated 6.6 years ago by
Rory Stark
★ 5.1k • written 6.6 years ago by
rbronste
▴ 60
0
votes
3
replies
2.7k
views
DESeq2 MA plot look different
deseq2
maplot
updated 6.6 years ago by
Michael Love
41k • written 6.6 years ago by
jshouse
▴ 10
3
votes
6
replies
1.8k
views
Clarification MAplot and FDR in EdgeR
edgeR
MAplot
rnaseq
differential gene expression
updated 7.7 years ago by
Gordon Smyth
50k • written 7.7 years ago by
joseph.bergenstrahle
• 0
0
votes
0
replies
1.2k
views
error while running MAplot
MAplot
rnaseq
cummerbund
8.0 years ago
kritikamish99
▴ 10
16 results • Page
1 of 1
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Replies
Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
by
Michael Love
41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO
by
fernanda.backsouza
▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Answer: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
swbarnes2
★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error
by
James W. MacDonald
65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Votes
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
C: when to apply quantile normalization with voom in limma/voom framework with RNA-
A: How to know if I should use voomWithQualityWeights() or not?
A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom
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