[BioC] arrayQualityMetrics

[Steve Taylor]

Hi,

I am using arrayQualityMetrics and have a few questions.

1) When creating the NChannelSet I am using Bluefuse data (the AMPCH1 and AMPCH2 columns) which do not have background readings, so I am reading it in like this

assayData = with(RG, assayDataNew(R=R, G=G))

This seems to be ok but I was wondering if this has any knock on effects I should be aware of, either with processing or report generation?

2)RNA Integrity Number (RIN) 	
This seems to be required for phenoData, which is required to create the NChannelSet. If I don't have these values what should I do?

3)I like the fact there are descriptions of different QC methods in the report. What would also be helpful is if there were some example reports online to compare what good/bad reports look like. Are 
there any available?

Thanks for any help,

Steve
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Weatherall Institute of Molecular Medicine/Sir William Dunn School
Oxford University