[BioC] How does one deal with spatial effects detected on single channel microarrays?

[Scott Robinson [guest]]

Dear all,

I have been doing pre-processing & QC of a number of CEL files (from Affymetrix U133+ v2.0 chips), basing things loosely on this tutorial (http://bioinformatics.knowledgeblog.org/2011/06/20/analysing-microarray-data-in-bioconductor/), and on some past experience of other microarray technologies.

Many tutorials seem to deal with indentification of spatial effects but do not discuss how to handle them. As such I have been having difficulty finding methods directed at spatial normalization in single-channel arrays (OLIN, smida, marray and nnNorm all seem to be written for dual-channel arrays). Can anyone please suggest an appropriate package/method for single-channel Affy chips?

And are there cases where they should be excluded rather than normalized?

Some examples of my spatial artefacts:

http://postimg.org/image/kkfjt4o1j/
http://postimg.org/image/v5utre4zb/
http://postimg.org/image/yfdublign/

Of my 90 chips example 2 is the only one of that kind of pattern. The rest are mostly similar in form to the other 2 and similar patterns are seen in ~20 chips.

Thanks in advance,

Scott

 -- output of sessionInfo(): 

R version 3.0.1 (2013-05-16)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United Kingdom.1252 
[2] LC_CTYPE=English_United Kingdom.1252   
[3] LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.1252    

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] limma_3.16.7          sparcl_1.0.3          lattice_0.20-23      
 [4] corrplot_0.71         affyPLM_1.36.0        preprocessCore_1.22.0
 [7] simpleaffy_2.36.1     gcrma_2.32.0          genefilter_1.42.0    
[10] affy_1.38.1           Biobase_2.20.1        BiocGenerics_0.6.0   

loaded via a namespace (and not attached):
 [1] affyio_1.28.0        annotate_1.38.0      AnnotationDbi_1.22.6
 [4] BiocInstaller_1.10.3 Biostrings_2.28.0    DBI_0.2-7           
 [7] grid_3.0.1           IRanges_1.18.3       RSQLite_0.11.4      
[10] splines_3.0.1        stats4_3.0.1         survival_2.37-4     
[13] XML_3.98-1.1         xtable_1.7-1         zlibbioc_1.6.0

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