[BioC] display spots of multiple control status (maControls)

Foata,Francis,LAUSANNE,NRC/N&H francis.foata at rdls.nestle.com
Wed Nov 26 18:43:49 MET 2003


Hello,

I want to hightligh spots (with different "controls" status) on MA plots.

Here is a print screen of the control section of my mArrayRaw object

Control spots: 
There are   5 types of controls : 
Blank Empty    na    OK   RNC 
  960   225   334 21521   192 

As you can see there is 5 differents levels of control spot (Blank, Empty,
na, OK and RNC). For highliting ONE specific category of control spots it's
working well :

# example with For N/A spots

	na.spots <- maText(subset=maControls(christian.raw[,1]) == "na",
col="Red", labels="O")
	maPlot(christian.raw[,1], text.func = na.spots, legend.func = NULL,
lines.func = NULL)


To highlight spots of multiple control status (for example "NA" OR "Empty")
I've tried this R code:

	na.empty.spots <- maText(subset=(maControls(christian.raw[,1]) ==
"na" || "Empty"), col="Red", labels="O")
	maPlot(christian.raw[,1], text.func = na.empty.spots, legend.func =
NULL, lines.func = NULL)

Result:

Error in maControls(christian.raw[, 1]) == "na" || "Empty" :  invalid `y'
type in `x || y'

I tried too ("na" || "Empty" ------> "na || Empty") :

	na.empty.spots <- maText(subset=(maControls(christian.raw[,1]) ==
"na || Empty"), col="Red", labels="O")
	maPlot(christian.raw[,1], text.func = na.empty.spots, legend.func =
NULL, lines.func = NULL)

I get a MA plot without any hightlighed spots.

Does anybody know how to handle this problem?

Regards,


Francis



More information about the Bioconductor mailing list