[BioC] Specifying wells in normalization for cellHTS2

[ligia at ebi.ac.uk]

Hi Steve,

You have to specify the negative controls in a way that is consistent with
how they were annotated by the plate configuration file.

The default annotation for negative and positive controls is "neg" and
"pos", respectively, and such annotation is assumed by "normalizePlates"
when you choose to perform a controls-based normalization (i.e. you can
omit the arguments negControls and/or posControls in this case, since they
are by default set to posControls="pos" and negControls="neg").

Alternatively, you can use a more specific annotation for the controls in
the plate configuration file, such as the name of the genes they target,
etc., which is useful when you use different types of positive or negative
controls. In this case, and as indicated in the help page of
"normalizePlates", you can find an example on how to set the arguments
"negControls" (and/or "posControls") in the help page of
"summarizeChannels".

I hope that I've answered your question.

Cheers,
Ligia


> Hi,
>
> I would like to specify normalization based on certain negative control
> wells using the package cellHTS2. I am trying:
>
> xn<-normalizePlates(x,scale="multiplicative",log=FALSE,method="negatives",varianceAdjust="none",negControls=c("B12","C01","C12","D01","D12","E01","F01"))
>
> but get:
>
> Error in checkControls(y = negControls, len = nrChannel, name =
> "negControls") :
>    'negControls' should be a vector of regular expressions with length 1
>
> What's the best way to do this?
>
> Thanks for any help,
>
> Steve
>
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