[BioC] arrayQualityMetrics stringency & co
yannick.wurm at unil.ch
Thu Oct 16 10:18:49 CEST 2008
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
standardGeneric for "arrayQualityMetrics" defined from package
function (expressionset, outdir = getwd(), force = FALSE,
do.logtransform = FALSE,
split.plots = FALSE, intgroup = "Covariate")
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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