[BioC] MA plot for highthrouput qPCR array, shows bias?

[Heidi Dvinge]

Hi Ali,

> Hi everyone,
>
> Newbie here. I was wondering whether an MA plot for highthrouput qPCR
> array (~760 genes) shows the bias?

The best way to find out is probably to try it :). Remember that (for log2
values) M and A are simply defined as:
M = R - G
A = (R + G)/2
You can therefore calculate these values for whatever samples you have,
either assigning 'R' and 'G' to two different samples, or for example let
one of them be the mean across all samples.

Alternatively, there is an increasing number of qPCR-specific packages in
Bioconductor. HTqPCR contains a number of functions for visualising data
quality + potential biases and for normalising or removing 'bad' samples.
In addition, if you do a search on
http://bioconductor.org/packages/release/bioc/ there's more packages you
might be interested in.

HTH
\Heidi

> Especially because in contrary to
> array  results, lower expression values have higher "signals". Would
> transformation of results help? How may I do that?
>
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