Moderator: Kevin Blighe
Kevin Blighe ♦ 66k
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Posts by Kevin Blighe
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Comment:
C: How to plot figure?
... The bottom part is just a heatmap - check the methods to see what it says. Then, the entire figure panels are likely pieced together manually ...
written 10 days ago by
Kevin Blighe ♦ 66k
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... Use the FDR column instead of the nominal p-value column. ...
written 12 days ago by
Kevin Blighe ♦ 66k
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1.4k
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Comment:
C: getBM error while using bioMart
... I see. What is the output of:
str(TPM_countdata$ensembl)
?
Also, from where are you running this command (on a cluster)?
...
written 16 days ago by
Kevin Blighe ♦ 66k
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Comment:
C: getBM error while using bioMart
... Hi, can you please try just:
ensembl = useEnsembl(biomart = "ensembl", dataset = "hsapiens_gene_ensembl")
Also, which version of R and *biomaRt* are you using? ...
written 16 days ago by
Kevin Blighe ♦ 66k
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... Yes, *PCAtools* can do this: Determine the variables that drive variation among each PC
But, let me know how you have currently done your PCA? ...
written 16 days ago by
Kevin Blighe ♦ 66k
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Answer:
A: Reorganize the clusters
... Boa tarde,
Tem que definir os agrupamentos fora do função `Heatmap()`, como faço aqui: / You have to define the clusters outside of the `Heatmap()` function, as I do here:
- https://github.com/kevinblighe/E-MTAB-6141
Depois/ Then (after), follow the advice here: https://www.biostars.org/p/306473 ...
written 18 days ago by
Kevin Blighe ♦ 66k
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... Thank you Sir. You got it working? ...
written 19 days ago by
Kevin Blighe ♦ 66k
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135
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... Please see the vignette, which I personally wrote: https://bioconductor.org/packages/devel/bioc/vignettes/EnhancedVolcano/inst/doc/EnhancedVolcano.html#over-ride-colour-andor-shape-scheme-with-custom-key-value-pairs ...
written 20 days ago by
Kevin Blighe ♦ 66k
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... I am sorry - this is difficult for me to debug while remote. You will have to go back through your code. Keep in mind that this type of work is quite advanced. ...
written 20 days ago by
Kevin Blighe ♦ 66k
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... That is for the cross-validated R2? What was the output of `DAAG::cv.lm`?
You could avoid `crossval()` for now. How does the plot for Predicted versus Real values appear? ...
written 20 days ago by
Kevin Blighe ♦ 66k
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For A simple tutorial for a complex ComplexHeatmap
Teacher
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For A: problem in generating correlation heatmap with significance level
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