[BioC] Array quality question

Wolfgang Huber huber at ebi.ac.uk
Fri Aug 29 19:30:40 CEST 2008


Hi Oliver

1. what happens to the variance-mean plot when you remove the bad array(s)?

2. how does it look like when you use RMA instead of MAS5? (and
possibly, vsnrma)

3. The behavior of the variance-mean plot in the upper intensity range
is indicative of likely saturation effects.

4. One possible explanation for the behavior of the variance-mean plot
in the lower intensity range could be that different (batches of) arrays
have quite different background intensity distributions.

Best wishes
 Wolfgang

------------------------------------------------------------------
Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber


28/08/2008 18:53 Oliver Hofmann scripsit
> Dear all,
> 
> 
> I've been struggling with a quality control for a set of Affymetrix
> hgu133a2 chips created from seven different samples (two chips each, one
> original sample, the second one with a subpopulation of FACS-sorted
> cells). Lacking experience with array analysis I was hoping someone from
> the list would be able to identify what the problem might be.
> 
> I've posted the standard QCReport over here (not sure the list can
> handle attachments?):
> 
>   http://fiamh.info/hsph/QualityControl.pdf
> 
> To a newbie like me it _looks_ fairly okay. From RNA degradation plots I
> already knew that E_neg (chip 9) was a problem and it's been discarded;
> what seemed odd is the downscaling of all chips (page 3). Also, the
> probesets for the cell surface marker used in the FACS sorting exhibited
> a very strong foldchange (between 20-30 times, to be expected) whereas
> no other probeset showed more than 2-3-fold up- or down-regulation.
> 
> What confuses me is the arrayQualityMetrics report. The variance mean
> dependency chart shows quite a bit of variation for the lower ranks:
> 
>   http://fiamh.info/hsph/report_sample/QMreport.html
> 
> Mini-script is attached below. I was merely wondering whether the QC is
> still within normal (expected) boundaries, or whether they warrant
> further investigations.
> 
> 
> Thanks!
> 
> -- Oliver
> 
> ----8<----
> library(affyQCReport);
> library(simpleaffy);
> library(arrayQualityMetrics)
> 
> msc.data <- read.affy('covdesc', path='../CEL Files')
> QCReport(msc.data, file = "QualityControl.pdf");
> 
> msc.eset <- call.exprs(msc.data, "mas5");
> arrayQualityMetrics(expressionset=msc.eset,
>                     outdir='report_sample',
>                     force=TRUE,
>                     do.logtransform=FALSE)
> 
> -----8<------
>> sessionInfo()
> R version 2.7.1 (2008-06-23)
> i386-apple-darwin8.10.1
> 
> locale:
> C/UTF-8/C/C/C/C
> 
> attached base packages:
>  [1] grid      splines   tools     stats     graphics  grDevices utils
>  [8] datasets  methods   base
> 
> other attached packages:
>  [1] arrayQualityMetrics_1.6.1 beadarray_1.8.0
>  [3] latticeExtra_0.5-1        vsn_3.6.0
>  [5] limma_2.14.5              affyQCReport_1.18.0
>  [7] geneplotter_1.18.0        annotate_1.18.0
>  [9] AnnotationDbi_1.2.2       RSQLite_0.6-9
> [11] DBI_0.2-4                 lattice_0.17-8
> [13] RColorBrewer_1.0-2        affyPLM_1.16.0
> [15] xtable_1.5-2              simpleaffy_2.16.0
> [17] gcrma_2.12.1              matchprobes_1.12.0
> [19] genefilter_1.20.0         survival_2.34-1
> [21] affy_1.18.2               preprocessCore_1.2.0
> [23] affyio_1.8.0              Biobase_2.0.1
> 
> loaded via a namespace (and not attached):
> [1] KernSmooth_2.22-22
> 
> 
> 
> 
>



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