User: maria2019

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maria201980
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Posts by maria2019

<prev • 66 results • page 1 of 7 • next >
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How to generate CpG REGIONs file to run DMR analysis with methylkit?
... 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 ...
methylkit dmr rrbs cpg-regions written 4 days ago by maria201980 • updated 3 days ago by Charles Warden7.5k
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Comment: C: How to plot 2 different symbols in a 3D PCA plot generated by rgl-plot3D
... 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 maria201980
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Comment: C: How to plot 2 different shapes in 3D PCA plots generated by rgl plot3D
... Thanks for your comment. I just tried plot3D. The problem is that I cannot rotate the generated figure ...
written 8 days ago by maria201980
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How to plot 2 different symbols in a 3D PCA plot generated by rgl-plot3D
... 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 ...
rgl 3d_pca rna-seq plot3d written 9 days ago by maria201980
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Comment: A: Why do I get different results for PC1 from plotPCA(DESeq2) and prcomp?
... 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 maria201980
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Answer: C: What is the best R package to plot eye catching 3D PCA plots?
... I realized that I can plot better figures using rgl plot3d! Thanks ...
written 12 days ago by maria201980
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Why do I get different results for PC1 from plotPCA(DESeq2) and prcomp?
... 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? ...
deseq2 pca plotpca prcomp written 12 days ago by maria201980
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What is the best R package to plot eye catching 3D PCA plots?
... 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? ...
pca plot R written 13 days ago by maria201980
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Comment: C: statistics method to find the relation between multiple variables of 50 samples
... 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 maria201980
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Comment: C: statistics method to find the relation between multiple variables of 50 samples
... 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 maria201980

Latest awards to maria2019

Scholar 12 days ago, created an answer that has been accepted. For C: What is the best R package to plot eye catching 3D PCA plots?
Popular Question 4 weeks ago, created a question with more than 1,000 views. For Strange MT% in 10X scRNA-seq data analysis
Supporter 4 months ago, voted at least 25 times.

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