[BioC] HTqPCR (plotCtOverview) problem

[Michael Muratet]

Greetings

I have R 2.11, BioC 2.6 and HTqPCR 1.2 (see session info at the end).

I created a qPCRset object by using rbind() to concatenate four pairs  
of dissimilar cards for each experimental condition and then cbind()  
to concatenate the four objects into one:

WT_time1.a |
WT_time1.b |---> WT_time1
MT_time1.a |
MT_time1.b |---> MT_time1
WT_time2.a |                           ---> s2010004660
WT_time2.b |---> WT_time2
MT_time2.a |
MT_time2.b |---> MT_time2

I set g <- c("MammU6") which is a endogenous control gene.

I then tried to plotCtOverview(s2010004660, genes=g,  
groups=sampleNames(qPCRset), conf.int=TRUE) and got

 > plotCtOverview(s2010004660, genes=g, conf.int=TRUE)
Error in if (del == 0 && to == 0) return(to) :
   missing value where TRUE/FALSE needed

Here's the object info:

 > s2010004660
An object of class "qPCRset"
Size:  768 features, 4 samples
Feature types:		 Endogenous Control, Target
Feature names:		 mmu-let-7b-4373168 mmu-let-7c-4373167 mmu- 
let-7d-4395394 ...
Feature classes:	
Feature categories:	 OK, Undetermined
Sample names:		 WT_4wks MT_4wks WT_17wks ...

Could it be that the Feature classes slot is empty?

Here's session info:

 > sessionInfo()
R version 2.11.0 (2010-04-22)
i386-apple-darwin9.8.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] HTqPCR_1.2.0       limma_3.4.0        RColorBrewer_1.0-2  
Biobase_2.8.0      MASS_7.3-5

loaded via a namespace (and not attached):
[1] affy_1.26.0           affyio_1.16.0         gdata_2.7.1            
gplots_2.7.4          gtools_2.6.1          preprocessCore_1.10.0
[7] tools_2.11.0

Thanks

Mike

Michael Muratet, Ph.D.
Senior Scientist
HudsonAlpha Institute for Biotechnology
mmuratet at hudsonalpha.org
(256) 327-0473 (p)
(256) 327-0966 (f)

Room 4005
601 Genome Way
Huntsville, Alabama 35806