Question: PCA for multiple transcriptome-assemblies
0
gravatar for Shahzad
12 months ago by
Shahzad10
Pakistan
Shahzad10 wrote:

Hi Can we perform Principal component analysis PCA for multiple transcriptome-assemblies to show the shared similarity between them?

R rna-seq next-gen assembly • 355 views
ADD COMMENTlink written 12 months ago by Shahzad10
1

Yes, you can plot a PCA on the normalized read-count or expression data of the transcriptome-assemblies.

ADD REPLYlink written 12 months ago by sangram_keshari230

What exact input data do you have? - just the assembled transcript sequences in FASTA format?

ADD REPLYlink written 12 months ago by Kevin Blighe65k

I have gene count data for PCA analysis, can you suggest the pipeline in R for the PCA analysis

ADD REPLYlink written 6 months ago by harshraje1930

In R you can simply Principal Components Analysis

pca <- prcomp(read_count_df)

For plotting

library(ggfortify)  
autoplot(pca, loadings.label = TRUE)
ADD REPLYlink modified 6 months ago • written 6 months ago by sangram_keshari230
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