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CummeRbund: I can't create a dispersion plot - help please?

Hi all,

I am now somewhat familiar with cummeRbund and have all my plots already except for one: a dispersion plot. I know dispersionPlot only runs on a cuffData object, however I don;t know how to create a cuffData object. Ive looked at the cuffData help file but the usage is not clear to me.

My code

library("cummeRbund")

library("plyr")

library("Hmisc")

setwd("[pathto]/r_working_directory")

cuff <- readCufflinks(genome = 'rn6', gtfFile = "genes.gtf",rebuild = TRUE)

disp<-dispersionPlot(genes(cuff))

disp

So the code is successful (creates a "disp" value in the environment window)

however when i try to veiw it I get the following error:

Error in $<-.data.frame(*tmp*, "SCALE_X", value = 1L) : replacement has 1 row, data has 0 In addition: Warning message: In max(panels$ROW) : no non-missing arguments to max; returning -Inf

I really have no idea how to fix this. Do need to create a cuffData object, if so how? Or is there a simpler fix?

Thanks all in advance. Kenneth.

rna-seq cummerbund dispersionplot cuffdata class
• 2,837 views • link
written by BioinfGuru BioinfGuru

The gtf file is merged.gtf file from cuffmerge, right? If not, can you try with merge.gtf file?

• 1 views • link
written by Satyajeet Khare Satyajeet Khare

Right you are,.... I had the wrong gtf.......still didnt solve the problem though

• 1 views • link
written by BioinfGuru BioinfGuru

Can you check if cuff is created properly?

cuff

If it is made properly, you should see number of samples, genes, isoforms, TSS, CDSs etc.

• 1 views • link
written by Satyajeet Khare Satyajeet Khare

I've actually found out that it has to do with the versions I'm using. Thank you.

• 1 views • link
written by BioinfGuru BioinfGuru

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