[BioC] How to objectively evaluate chip quality?

[Nathan.Watson-Haigh at csiro.au]

Hi Mark,

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

Nathan

-----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'.

cheers,
Mark
-----------------------------------------------------
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:
>
http://bioconductor.org/packages/2.2/bioc/vignettes/simpleaffy/inst/doc/
> 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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