[BioC] HTqPCR plotting groups of interest

[Simon Melov]

If anyone can help, it would be great.

I want to plot different groups of interest in HTqPCR using some of the plot functions, and I've played around with plotting different ways a number of times, and cant get the plot functions in HTqPCR to display what I want. I've a large number of groups, and dont want to plot everything every time (plotting everything works just fine after Heidi's help).

#the plate6 CSV file links the sample ID to the group (Treatment) it belongs to#
 >plate6=read.csv("PlateG6.csv", header=TRUE, as.is=TRUE)
> head(plate6)
  Sample Treatment
1    NTC       NTC
2    L29       LFY
3    M10       MMO
4    C30       CFY
5    S15       SFO
6    S28       SMY
> group6=as.vector(t(plate6$Treatment))
> sample6=as.vector(t(plate6$Sample))
> raw6=readCtData(files="Chip6NTC.csv", format="BioMark", n.features=48, n.data=48, samples=sample6)
> g=featureNames(raw6)[1]
> g
[1] "TUB"
> plotCtOverview(raw6, genes=g, col=rainbow(48), group=group6, Legend=FALSE)
#works fine, plots the first gene Tubulin nicely, however, now I want to compare my NTC group with my LFY group (listed in "Treatment" above)#
#I've tried the below to just plot one group, the "NTC" group, and it doesnt work (I'm not clear why, whatever is being plotted is not correct), #
#not sure how to plot just two groups with this function (or three, or however many I want)#

 >plotCtOverview(raw6, genes=g, col=rainbow(48), group=group6[1], legend=FALSE)

thanks in advance

Simon