User: e.rempel
e.rempel • 430
- Reputation:
- 430
- Status:
- Trusted
- Location:
- Germany, Heidelberg, COS
- Last seen:
- 6 hours ago
- Joined:
- 2 years, 5 months ago
- Email:
- e*******@dkfz-heidelberg.de
Statistician/bioinformatician.
Posts by e.rempel
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1
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answer
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... I will post my comment on the update here:
you could try run
heatmap.2(mat, ...)
directly after
mat <- assay(rld)[ topVarGenes, ]
mat <- mat - rowMeans(mat)
...
written 23 hours ago by
e.rempel • 430
5
votes
1
answer
125
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1
answers
... HI,
this line takes the top 500 genes with the highest variance. Per default, **order** is sorting in increasing order, thus the author of the code uses the minus sign (but she should have used just *order(..., decreasing = T)* ...
written 1 day ago by
e.rempel • 430
2
votes
1
answer
111
views
1
answers
Answer:
A: topGO allGenes argument
... Hi
you could use:
rownames(topTags(tr)@.Data[[1]]) ...
written 1 day ago by
e.rempel • 430
1
vote
3
answers
255
views
3
answers
Comment:
C: Filter by Fold change in DESeq2
... Just a comment: in my opinion, the right approach is to run `res <- results(dds, alpha=0.05)` and then filter based on *log2FoldChange* (eventually remove the rows with NAs, which can appear if the number of reads in one condition equals zero). Thus I would assume that 180 genes are what you are ...
written 21 days ago by
e.rempel • 430
1
vote
3
answers
255
views
3
answers
... Hi,
you could filter the **res** object directly in R
res <- res[res$log2FoldChange >= 1, ]
...
written 22 days ago by
e.rempel • 430
0
votes
5
answers
388
views
5
answers
Comment:
C: code for text file parsing
... Could you please explain what
> && !a[$0]++
does? ...
written 22 days ago by
e.rempel • 430
0
votes
3
answers
257
views
3
answers
... I agree that the interpreting of 5-way Venn Diagram is not easy. ...
written 25 days ago by
e.rempel • 430
0
votes
3
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257
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3
answers
... I am not sure whether plotting proportional 5-way Venn Diagram is even (mathematically) possible. You could also try a shiny [app][1] for plotting of Venn Diagrams.
[1]: http://jolars.co/eulerr/ ...
written 25 days ago by
e.rempel • 430
0
votes
3
answers
257
views
3
answers
... R-package **SystemPiper** offers the possibility to Plot 2-5 way Venn diagrams. E.g.
![VennDiagram][1]
The manual is available on [here][2]
[1]: http://www.imsbio.co.jp/RGM-files/R_BC/result/systemPipeR/vennPlot.Rd_005_medium.png
[2]: http://www.imsbio.co.jp/RGM/R_rdfile?f=systemPipeR/man/v ...
written 25 days ago by
e.rempel • 430
0
votes
3
answers
903
views
3
answers
Comment:
C: network with cytoscape
... Looks like someone joined Biostars just to make some advertising. ...
written 25 days ago by
e.rempel • 430
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For A: GO analysis using topGO Arabidopsis
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For C: Pheatmap error: 'gpar' element 'fill' must not be length 0 , what to do about
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