[BioC] arrayQualityMetrics stringency & co

Yannick Wurm yannick.wurm at unil.ch
Thu Oct 16 10:18:49 CEST 2008

Morning List,

I've been toying with arrayQualityMetrics which gives me a great  
overview of my data without too much work.

Several things are still unclear to me though:

	- how does it calculate the '*' that indicate that a chip may be  
bad. How stringent/conservative are they? Because several of my  
spotted cDNA chips show up as having issues, and now I'm unsure  
whether or not I should remove them from my analysis.

	- is there any way to "see inside" the package? I'd like to see how  
the stringency is calculated, and adapt some of the output  
formatting. But when I try to look inside, all I get is something  
called "environment":
		> arrayQualityMetrics

		standardGeneric for "arrayQualityMetrics" defined from package  
		function (expressionset, outdir = getwd(), force = FALSE,  
do.logtransform = FALSE,
			split.plots = FALSE, intgroup = "Covariate")
		<environment: 0x4882ad8>
		Methods may be defined for arguments: expressionset, outdir, force,  
do.logtransform, split.plots, intgroup
		Use  showMethods("arrayQualityMetrics")  for currently available ones.
	- on one NChannelSet containing 280 slides, arrayQualityMetrics  
didn't calculate the heatmap. But didn't display any error messages  
either. Possibly because of memory contraints on my 3GB mac?

Thanks for putting me on the track to resolving this.



          yannick . wurm @ unil . ch
Ant Genomics, Ecology & Evolution @ Lausanne

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