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volcanoplot
•
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0
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4
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1.2k
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Volcano plot becomes flipped when I add a third condition
DESeq2
volcanoplot
deseq
HELP
contrast
updated 14 months ago by
Basti
▴ 780 • written 14 months ago by
Michael
• 0
0
votes
1
reply
760
views
part of the volcano plot does not appear.
plot
volcano
volcanoplot
updated 14 months ago by
Basti
▴ 780 • written 14 months ago by
Sooni
▴ 10
0
votes
1
reply
573
views
Assigning the name of top 100 DE transcripts/genes to Volcano plot
limma
DEGreport
Volcanoplot
updated 16 months ago by
Gordon Smyth
50k • written 16 months ago by
Mohammad
• 0
3
votes
5
replies
2.0k
views
Volcano plot - select additional gene
EnhancedVolcano
RNASeqR
R
volcanoplot
updated 3.5 years ago by
Kevin Blighe
★ 3.9k • written 3.5 years ago by
camillab.
▴ 10
1
vote
5
replies
2.3k
views
Why the p value and logFC calculated by limma is so small
limma
volcanoplot
pvalue
logFC
updated 5.1 years ago by
Gordon Smyth
50k • written 5.1 years ago by
xingxd16
▴ 20
0
votes
4
replies
6.8k
views
Limma Volcano Plot Highlight Top Genes by Color
limma
microarray
volcanoplot
color
updated 5.5 years ago by
Gordon Smyth
50k • written 5.5 years ago by
dmm204
• 0
2
votes
4
replies
7.2k
views
Volcano Plot (highlighting top genes in a different color)
volcanoplot
updated 6.5 years ago by
thokall
▴ 160 • written 6.5 years ago by
Nithisha
▴ 10
0
votes
1
reply
1.0k
views
Pseudo-coloring DiffBind volcano plot
diffbind
chipseq
volcanoplot
ggplot2
updated 6.5 years ago by
Rory Stark
★ 5.2k • written 6.6 years ago by
rbronste
▴ 60
0
votes
2
replies
1.7k
views
Draw volcano plot by modifying contrast matrix (lumi package)
volcanoplot
design and contrast matrix
updated 6.6 years ago by
Gordon Smyth
50k • written 6.6 years ago by
marongiu.luigi
• 0
10
votes
3
replies
9.0k
views
Volcanoplot with limma - RAW P-values or Adj.P-Values
volcanoplot
limma
fdr
6.8 years ago • updated 3.4 years ago
tcalvo
▴ 90
5
votes
4
replies
6.7k
views
Volcano plot labeling troubles
limma
volcanoplot
updated 6.8 years ago by
Gordon Smyth
50k • written 9.5 years ago by
mccallionc403
• 0
0
votes
2
replies
1.2k
views
volcano plot in Limma
limma
volcanoplot
updated 8.0 years ago by
Aaron Lun
★ 28k • written 8.0 years ago by
mheydarpour
▴ 10
7
votes
4
replies
5.7k
views
Gene symbols on MA-plot
limma
plot.MA
volcanoplot
oligo
updated 8.8 years ago by
Gordon Smyth
50k • written 8.8 years ago by
Gabriel Nathan Kaufman, Mr
▴ 60
2
votes
2
replies
3.1k
views
cummeRbund change point size in volcano plot
cummerbund
ggplot2
size
r
volcanoplot
updated 9.4 years ago by
James W. MacDonald
65k • written 9.4 years ago by
ianmisner17
▴ 20
14 results • Page
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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
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?
Answer: How to retrieve gene ontology GO class from gene list?
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