Question: CummeRbund: I can't create a dispersion plot - help please?
1
gravatar for YaGalbi
2.7 years ago by
YaGalbi1.4k
Biocomputing, MRC Harwell Institute, Oxford, UK
YaGalbi1.4k wrote:

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.

ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by YaGalbi1.4k
1

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

ADD REPLYlink modified 2.7 years ago • written 2.7 years ago by Satyajeet Khare1.3k

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

ADD REPLYlink written 2.7 years ago by YaGalbi1.4k

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.

ADD REPLYlink written 2.7 years ago by Satyajeet Khare1.3k

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

ADD REPLYlink written 2.7 years ago by YaGalbi1.4k
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