[BioC] HTqPCR problems

[Simon Melov]

Thanks!

I will work on it some more, didn't realize groups was defined by vector.


On Jun 26, 2012, at 12:48 PM, Heidi Dvinge <heidi at ebi.ac.uk> wrote:

>> Hi,
>> I'm having some troubles selectively sub-setting, and graphing up QPCR
>> data within HTqPCR for Biomark plates (both 48.48 and 96.96 plates). I'd
>> like to be able to visualize specific genes, with specific groups we run
>> routinely on our Biomark system. Typical runs are across multiple plates,
>> and have multiple biological replicates, and usually 2 or more technical
>> replicates (although we are moving away from technical reps, as the CVs
>> are so tight).
>> 
>> Can anyone help with this? Heidi?
>> 
>> raw6=readCtData(files="Chip6.csv", format="BioMark", n.features=48,
>> n.data=48, samples=samples)
>> #Ive read the samples in from a separate file, as when you read it in, it
>> doesnt take the sample names supplied in the biomark output#
>> #Next, I want to plot genes of interest, with samples of interest, and I'm
>> having trouble getting an appropriate output#
>> 
>> g=featureNames(raw6)[1:2]
>> plotCtOverview(raw6, genes=g, groups=groupID$Treatment, col=rainbow(5))
>> 
>> #This plots 1 gene across all 48 samples#
>> #but the legend doesnt behave, its placed on top of the plot, and I cant
>> get it to display in a non-overlapping fashion#
>> #I've tried all sorts of things in par, but nothing seems to shift the
>> legend's position#
>> 
> As the old saying goes, whenever you want a job done well, you'll have to
> do it yourself ;). In this case, the easiest thing is probably to use
> legend=FALSE in plotCtOverview, and then afterwards add it yourself in the
> desired location using legend(). That way, if you have a lot of different
> features or groups to display, you can also use the ncol parameter in
> legend to make several columns within the legend, such as 3x4 instead of
> the default 12x1.
> 
> Alternatively, you can use either xlim or ylim in plotCtOverview to add
> some empty space on the side where there's then room for the legend.
> 
>> #I now want to plot a subset of the samples for specific genes#
>>> LOY=subset(groupID,groupID$Treatment=="LO" | groupID$Treatment== "LFY")
>>> LOY
>>   Sample Treatment
>> 2     L20       LFY
>> 5     L30       LFY
>> 7     L45        LO
>> 20    L40        LO
>> 27    L43        LO
>> 33    L29       LFY
>> 36    L38        LO
>> 40    L39        LO
>> 43    L23       LFY
>> 
>> 
>>> plotCtOverview(raw6, genes=g, groups=LOY, col=rainbow(5))
>> Warning messages:
>> 1: In split.default(t(x), sample.split) :
>>  data length is not a multiple of split variable
>> 2: In qt(p, df, lower.tail, log.p) : NaNs produced
>>> 
> 
> Does it make sense if you split by groups=LOY$Treatment? It looks like the
> object LOY itself is a data frame, rather than the expected vector.
> 
> Also, you may have to 'repeat' the col=rainbow() argument to fit your
> number of features.
> 
>> 
>> #it displays the two groups defined by treatment, but doesnt do so nicely,
>> very skinny bars, and the legend doesnt reflect what its displaying#
>> #again, I've tried monkeying around with par, but not sure what HTqPCR is
>> calling to make the plots#
>> 
> If the bars are very skinny, it's probably because you're displaying a lot
> of features. Nothing much to do about that, except increasing the width or
> your plot :(.
> 
> \Heidi
> 
>> please help!
>> 
>> thanks
>> 
>> Simon.
>> 
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>> 
> 
>