[BioC] HTqPCR (plotCtOverview) problem

[Michael Muratet]

On Apr 30, 2010, at 2:42 PM, Heidi Dvinge wrote:

> 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?

Thanks Heidi

Here's the traceback():

 > plotCtOverview(s2010004660, genes=g, conf.int=TRUE)
Error in if (del == 0 && to == 0) return(to) :
   missing value where TRUE/FALSE needed
 > traceback()
3: seq.default(1.5, ncol(SD) * (nrow(SD) + 1), nrow(SD) + 1)
2: seq(1.5, ncol(SD) * (nrow(SD) + 1), nrow(SD) + 1)
1: plotCtOverview(s2010004660, genes = g, conf.int = TRUE)

conf.int = FALSE it makes the plot without complaining. Actually, it  
makes the plot in the first case, too, it just doesn't draw error bars.

Thanks again for the package and the help

Mike
>
> \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
>>
>>
>>
>>
>>
>
>

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