[BioC] HTqPCR (plotCtOverview) problem

[Heidi Dvinge]

>
> 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.
>
Hm, so for some reason it can't calculate a standard deviation for your
qPCRset. However it should work even if SD returns NA.

Do your have replicate genes in your set? And what happens if you say e.g.
groups=c("A", "A", "B", "B")?

\Heidi

> 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
>
>
>
>
>