Heidi Dvinge heidi at ebi.ac.uk
Thu Jun 23 18:43:52 CEST 2011

Hello Marco,

> Dear all,
> I am running  HTqPCR  to analyse tilda.
> I run 3 TLDA, in each cards thre are 2 samples, but the samples are
> diffrerents in the cards
> card1: Control and LPS
> card2: LPS and PMA
> card3: Control and LPS
Actually, it doesn't matter whether the samples are the same or not.
Instead of having a data matrix with 384 x 3 values you want 192 x 6. The
content of these 6 columns can vary.
> If the three carder would have the same sample, I have no problem as
> shown in the vignette
> sample2a.order <- factor(rep(c("Control","LPS"), each=192))
> qPCRnew2[1] <- changeCtLayout(raw, sample.order = sample2a.order)
The sample2a.order object doesn't have to contain the real sample names at
all. It's merely to indicate where on the qPCR card the different samples
are located. For example, you can imagine a card with 8 rows of wells. The
two samples can then either be loaded into rows 1-4 and 5-8, or 1,3,5,7
and 2,4,6,8 depending on the layut of the card.

In you case, you can therefore just rename the samples as required. E.g.

sample2a.order <- factor(rep(c("X","Y"), each=192))
qPCRnew <- changeCtLayout(qPCRraw[,1:3], sample.order = sample2a.order)
sampleNames(qPCRnew) <- c("Control", "LPS", "LPS", "PMA", "Control", "LPS")

In this case you'd probably want to use e.g. clusterCt(qPCRnew, type =
"samples"), to check whether the re-formatted qPCRset object cluster by
biological samples or by the original 3 cards.


> but my situation is different
> Can you help me?
> thank you
> marco

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