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Plot table with all replicates in cuffdiff output with cummeRbund

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

r cufflinks cuffdiff cummerbund plot
• 4,785 views • link
updated by zx8754 zx8754 • written by sindrelee • sindrelee

1 answer

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

• 1,019 views • link
written by Martombo Martombo

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