SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
cummeRbund MDS and PCA plot explanation Sushil Bioinformatics 1 07-29-2015 08:07 PM
CummeRbund: subset Cuffdiff genes based >1 isoform or other features beeman Bioinformatics 0 10-01-2014 10:11 PM
cummeRbund PCA plot glados Bioinformatics 1 04-22-2014 04:45 AM
cummeRbund PCA plot glados RNA Sequencing 0 04-15-2014 01:08 PM
Limit findSimilar() to a subset of genes in the whole Cufflinks data set [cummeRbund] Gus Bioinformatics 1 03-23-2014 11:24 AM

Reply
 
Thread Tools
Old 07-10-2015, 04:56 AM   #1
vilperte
Junior Member
 
Location: Brazil

Join Date: Aug 2014
Posts: 5
Default PCA plot in cummeRbund with subset genes

Hello all,

I'm trying to create a PCA plot with my data. I managed to create it with all my genes using the standard script:

genes.PCA<-PCAplot(genes(cuff), "PC1","PC2")


However, I would like to create the plot with a subset of those gene, e.g. the differentially expressed (DE) genes. I've created a subset for the DE genes as followed:

gene_diff_data<-diffData(genes(cuff))
sig_gene_data<-subset(gene_diff_data, (significant=='yes'))
sig_genes<-getGenes(cuff, sig_gene_data$gene_id)


When I try to create the PCA with the new subset, it does not work.

genes.PCA<-PCAplot(genes(sig_genes), "PC1","PC2")
Error in PCAplot(genes(sig_genes), "PC1", "PC2") :
error in evaluating the argument 'object' in selecting a method for function 'PCAplot': Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘genes’ for signature ‘"CuffGeneSet"’


Since my skills are very basic in R, could anyone tell me what I am doing wrong?

Thanks!

Best,

Vini
vilperte is offline   Reply With Quote
Reply

Tags
cummerbund, cummerbund plots, pca plot

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 11:20 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO