[BioC] How to objectively evaluate chip quality?

Nathan.Watson-Haigh at csiro.au Nathan.Watson-Haigh at csiro.au
Mon Jul 21 00:58:07 CEST 2008

Hi Mark,

Unfortunately, I have no experience of the Exon ST arrays, so can't give
any specific help...sorry.


-----Original Message-----
From: Mark Cowley [mailto:m.cowley0 at gmail.com] 
Sent: Monday, 21 July 2008 8:44 AM
To: Watson-Haigh, Nathan (LI, Rock. Rendel)
Cc: bioconductor list
Subject: Re: [BioC] How to objectively evaluate chip quality?

Thanks for your post Nathan,
I was hoping you could comment on the applicability of these QC  
metrics for the new Gene/Exon ST arrays?
In my experience, a number of the 3' IVT QC metrics can no longer can  
be calculated, at least not 'out of the box'.

Mark Cowley, BSc (Bioinformatics)(Hons)

Peter Wills Bioinformatics Centre
Garvan Institute of Medical Research, Sydney, Australia

On 16/07/2008, at 9:20 AM, <Nathan.Watson-Haigh at csiro.au>
<Nathan.Watson-Haigh at csiro.au 
 > wrote:

> Affymetrix provide several different metrics which can be utilised to
> see if your arrays are of good enough quality. However, the actual
> cut-off used is always subjective and can only be used as a guide.
> Generally speaking, you spend quite a good proportion of your  
> microarray
> analysis doing "Quality control through Data Exploration". As such,  
> it's
> quite a subjective thing, and you need to produce and explore lots of
> different graphs etc in order to get a good picture about the  
> quality of
> your arrays. Again, in general, you shouldn't base your opinion about
> the quality of an array on a single metric, but use several to inform
> you about the quality.
> Some specifics about the plots which I use routinely...
> 1) I use affyPLM to plot pseudo-images of the arrays with the  
> "weights".
> This will help you to visualise if any arrays are odd-ones out and  
> have
> poor hybridisation due to bubbles on the chip etc. See
> http://plmimagegallery.bmbolstad.com/ for examples of really bad  
> chips.
> 2) I use the "border elements plot" of the AffyQCReport (or a version
> I've altered) - again, helps to visualise how consistent hybridisation
> is around the edges of the arrays
> 3) The RNA degradation plot AffyRNAdeg() from the affy package
> 4) The Affymetrix quality control plot from qc() of the simpleaffy
> package
> 5) The spike-in control probes table produced by spikeInProbes() from
> the simpleaffy package
> 6) An Eisen plot produced by the made4 package.
> 7) A PCA plot produced by plotPCA() and a scree plot from the
> affycoretools package
> 8) A NUSE plot and RLE plot produced by the affyPLM package
> 9) A MAD plot produced by affyQAReport() of the affyQCReport package
> 10) A plot of the SD against the ranked mean intensity of probes using
> meanSdPlot() from the vsn package
> 11) A density plot of the PM probes using plotDensity.AffyBatch() of  
> the
> affy package
> 12) Boxplots of the PM probes using boxplot()
> I do all the above for raw data and then I do the normalisation and
> repeat plots 2, 6, 7, 9, 11 and 12. Then I calculate the gene  
> expression
> summaries and use limma to get differentially expressed genes. I use
> heatplot() from the made4 package to create heat plots of the
> Differentially expressed genes.
> So you can see I do a lot of diagnostic/QC/QA plots to explore the  
> data
> and to help inform me as to whether any of the arrays should be thrown
> out. Be careful not to throw out data just because it doesn't sit well
> with your expectations, you need to be able to justify why any array  
> is
> discarded, and simply saying that it's an outlier in just one metric  
> is
> not usually good enough.
> Here's a useful link:
> QCandSimpleaffy.pdf
> Hope this helps,
> Nathan
> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch
> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of simona
> dalle carbonare
> Sent: Wednesday, 16 July 2008 3:35 AM
> To: bioconductor mailing list
> Subject: [BioC] How to objectively evaluate chip quality?
> Hi,
> I have a question about quality assessment of microarray chips. Can
> somebody
> suggest me a quantitative metric to evaluate the chips and in  
> particular
> the
> plot about the quality of the chip (for example boxplot of intensity)?
> Thank you
> Simona
> 	[[alternative HTML version deleted]]
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