User: maria2019
maria2019 • 80
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Posts by maria2019
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... I have RRBS data that I have pre-processed using bismark. I wanna analyze DMR using methylkit. However, what I have is CpG calls from bismark methyl call and do not have CpG regions.
What package is the best to generate CpG regions so that I can run DMR analysis with methylkit?
** I have done DMC a ...
written 4 days ago by
maria2019 • 80
• updated
3 days ago by
Charles Warden ♦ 7.5k
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... True! thanks for your comment. I just tried it. The problem with plot3D is that I cannot rotate the generated figure. ...
written 6 days ago by
maria2019 • 80
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... Thanks for your comment. I just tried plot3D. The problem is that I cannot rotate the generated figure ...
written 8 days ago by
maria2019 • 80
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... Hi,
I have plotted a 3D PCA on my control vs treated samples using rgl.
I am interested in plotting control as SPHEREs and treatment as CUBEs. Is it possible to do that?
Below is my code:
library(rgl)
library(DESeq2)
rld_mat<- assay(rld)
select<- male_sig
rld_mat_m ...
written 9 days ago by
maria2019 • 80
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... Thanks kevin, ATpoint, and Asaf.
I tried the following code based on your comments and get the same result as plotPCA.
ntop <- 500
rv <- rowVars(assay(rld))
select <- order(rv, decreasing = TRUE)[seq_len(min(ntop, length(rv)))]
mat <- t( assay(rld)[select, ] )
p ...
written 12 days ago by
maria2019 • 80
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... I realized that I can plot better figures using rgl plot3d! Thanks ...
written 12 days ago by
maria2019 • 80
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5 follow
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... I have analyzed RNA-seq data with DESeq2 and am trying to plot a 3D PCA using rgl-plot3d.
I was trying to output PC1, PC2, and PC3 and then plot them. However, I realized that I get different results for PC1 (and PC2) when I try plotPCA (used with DESeq2) and prcomp.
What is the bug on my code?
...
written 12 days ago by
maria2019 • 80
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... I am looking for a package that plots the most beautiful 3D PCA plot for publication. I've been using rgl and Scatterplot3d but I want something much better than that. Cubemaker is very nice but does not allow to choose 2 different symbols in PCA (like circle and square). Any suggestion? ...
written 13 days ago by
maria2019 • 80
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... Thank you very much! I just tried it
One question, I also tried cor(mydata). I am gonna read through this more in depth but do you think I should get the same result for cor and lm? (mine are different when I try these data) ...
written 17 days ago by
maria2019 • 80
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... I am mostly interested to see, say if variable 1 increases, what happens at variable 2, etc. I know that PCA can show the separation between the groups but I need some more detailed method ...
written 17 days ago by
maria2019 • 80
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