[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