[BioC] limma neqc

[Wei Shi]

Dear Ina:

	You do not need to specify positive control probes. They were automatically read in when you use read.ilmn function to read in both regular probe data and control probe data. You can use the code below to see the numbers of regular probes, negative control probes and positive control probes:

x <- read.ilmn(files="probe profile.txt",ctrlfiles="control probe profile.txt", other.columns="Detection") # you will need to changes file names to the names of your files
table(x$genes$Status)

	The neqc function will then perform a quantile normalization for data included in x using all the probes (including regular probes, negative controls and positive controls). The two parameters negctrl and regular tell neqc what the identifiers of regular probes and negative control probes are. The negative control probes play a particular role in the background correction (normexp background correction aided by negative controls). By default, regular probes have an identifier of "regular". Negative control probes by default have an identifier of "negative" which was the identifier used by almost all the BeadChip data we have ever seen. The neqc function should work in most cases with its default setting.

	For more details, please refer to the limma user guide for analyzing Illumina BeadChip data (section 11.7).

	Hope this helps.

Cheers,
Wei

On Mar 23, 2011, at 6:40 AM, Ina Hoeschele wrote:

> Hi Gordon et al.,
>   I am confused about something - I am using limma neqc and according to a recent paper (Shi, Oshlack, Smyth 2010) the quantile normalization should be performed using both positive and negative control probes. But in the arguments for neqc one can specify the identifier for negative control probes and "regular" probes. So I set negctrl="negative" and regular="Gene". But this does not allow me to specify positive control probes?
> Many thanks, Ina
> 
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