Plot table with all replicates in cuffdiff output with cummeRbund

Question

[sindrelee]

Hi

Can someone help to do the following from the cummeRbund package:

I only want to plot a simple table by tweaking this command:

gl.iso.rep<-expressionPlot(isoforms(myGene),replicates=T)

Thank you so much

Answer 1

[Martombo]

expressionPlot is not going to produce a table but a line plot, showing the FPKM value of a gene or a feature for each condition of your analysis. if you're interested in plotting isoforms, your command is correct. what you need to do before this is: reading the cuffdiff results (while in the folder with the cuffData.db file) and get your gene(s) of interest from it (as shown in the example below)

cuff=readCufflinks(genome="hg19",gtfFile="human_ref_genes.gtf")
myGene=getGene(cuff,geneId="NM_201574")

then your command will work