[BioC] HTqPCR plotting groups of interest

[Heidi Dvinge]

Sorry all, pressed "send" too soon.

> Hi Simon,
>
>> If anyone can help, it would be great.
>>
>> I want to plot different groups of interest in HTqPCR using some of the
>> plot functions, and I've played around with plotting different ways a
>> number of times, and cant get the plot functions in HTqPCR to display
>> what
>> I want. I've a large number of groups, and dont want to plot everything
>> every time (plotting everything works just fine after Heidi's help).
>>
>> #the plate6 CSV file links the sample ID to the group (Treatment) it
>> belongs to#
>>  >plate6=read.csv("PlateG6.csv", header=TRUE, as.is=TRUE)
>>> head(plate6)
>>   Sample Treatment
>> 1    NTC       NTC
>> 2    L29       LFY
>> 3    M10       MMO
>> 4    C30       CFY
>> 5    S15       SFO
>> 6    S28       SMY
>>> group6=as.vector(t(plate6$Treatment))
>>> sample6=as.vector(t(plate6$Sample))
>>> raw6=readCtData(files="Chip6NTC.csv", format="BioMark", n.features=48,
>>> n.data=48, samples=sample6)
>>> g=featureNames(raw6)[1]
>>> g
>> [1] "TUB"
>>> plotCtOverview(raw6, genes=g, col=rainbow(48), group=group6,
>>> Legend=FALSE)
>> #works fine, plots the first gene Tubulin nicely, however, now I want to
>> compare my NTC group with my LFY group (listed in "Treatment" above)#
>
> Do you just want the Ct values of NTC relative to LFY? In that case have a
> look at the 'calibrator' parameter. As shown in the plotCtOverview
> examples, setting calibrator="LFY" will show all Ct values for other
> groups with LFY subtracted first.
>
>> #I've tried the below to just plot one group, the "NTC" group, and it
>> doesnt work (I'm not clear why, whatever is being plotted is not
>> correct),
>> #
>> #not sure how to plot just two groups with this function (or three, or
>> however many I want)#
>>
>>  >plotCtOverview(raw6, genes=g, col=rainbow(48), group=group6[1],
>> legend=FALSE)
>>
> The problem here is that you're inputting an object with *multiple*
columns, but
> you're only providing link from 1 column to a group. On top of that,
> plotCtOverview has no way of knowing which of the six columns you mean.
>
> For plotting just some of your groups, you therefore need to subset your
> qPCRset object. For example:
>
index <- group6  %in% c("SFY", "LFY", "CFY")
plotCtOverview(raw6[,index], genes=g, col=rainbow(48),
group=group6[index], Legend=FALSE)

NOw you're limiting your data to these 3 groups, but you still have a
column-to-group mapping for all your data.

HTH
\Heidi

>
>
>> thanks in advance
>>
>> Simon
>
>