csScatter: Error in match(x, table, nomatch = 0L)

Question

[megha.24may]

Hello everyone,

I am getting this error in csScatter command.

> csScatter(genes(cuff))
Error in match(x, table, nomatch = 0L) : 
  argument "x" is missing, with no default

Could anyone of you suggest something for this.

Thanks and regards
Megha varshney

[Sukhi Singh]

Crosspost: http://seqanswers.com/forums/showthread.php?t=59004

[Sukhi Singh]

Looks like problem with your genes(cuff) data object. I have never experienced this and hard to comment without checking at the actual data. Check if the object is empty (or it has any genes in).

For a comparison, use this as a reference.

a<-readCufflinks(system.file("extdata", package="cummeRbund"))# CuffSet object from data
genes<-a@genes #Create CuffData object for all genes
s<-csScatter(genes,'hESC','Fibroblasts',smooth=TRUE) #Create plot object
s #render plot object

[megha.24may]

As far as I know, then their no problem with object because I'm getting this return value and other plots like cdDensity and dispersion-plot with same object.

> genes(cuff)
CuffData instance with:
     59648 features and 3 samples

Answer 1

[h.mon]

From the csScatter help:

csScatter(object, x, y, logMode=TRUE, pseudocount=1.0, labels, smooth=FALSE, colorByStatus = FALSE, drawRug=TRUE, ...)

and:

x Sample name for x axis
y Sample name for y axis

As x and y do not have defaults, you have to pass them for the function call:

csScatter(genes(cuff), "X_axis_name", "Y_axis_name")

edit: please do not cross-post, it is not nice.