[BioC] HTqPCR (plotCtOverview) problem

[Heidi Dvinge]

Hello Mike,

> 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?
>
Feature classes shouldn't matter at all here. I can reproduce this using
the data sets included in HTqPCR (qPCRraw and qPCRpros) though. What does
traceback() say? And does the same happen when you use conf.int=FALSE?

\Heidi

> 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
>
>
>
>
>