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  • vilperte
    started a topic PCA plot in cummeRbund with subset genes

    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

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