[BioC] Array quality question

Oliver Hofmann ohofmann at hsph.harvard.edu
Thu Aug 28 19:53:08 CEST 2008


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





-- 
Research Fellow       Department of Biostatistics
                       Harvard School of Public Health



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