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

[Scott Robinson]

Dear Christian,

Thanks very much for the help. I especially like the "crop circles" artefact.

So is the idea that if you have a small spatial artefact it's probably going to affect only a small number of the probes in each probe set and therefore not affect the summarised values much? Do you only have to spatially normalize or remove a chip from analysis if the spatial artefact is quite large? Maybe if it covers 1/4 of the chip or something?

Thanks,

Scott

-----Original Message-----
From: cstrato [mailto:cstrato at aon.at] 
Sent: 02 September 2013 16:28
To: Scott Robinson [guest]
Cc: bioconductor at r-project.org; Scott Robinson
Subject: Re: [BioC] How does one deal with spatial effects detected on single channel microarrays?

Dear Scott,

Unlike cDNA arrays Affymetrix arrays use between 11 and 20 oligonucleotides per transcript. These oligos were placed in one line on the first Hu6800 array, but since a long time these oligos are scattered randomly across the whole array, in order to prevent spatial effects.

The images of your arrays are all ok.
You can see some weird examples at:
http://plmimagegallery.bmbolstad.com/

Best regards
Christian
_._._._._._._._._._._._._._._._._._
C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
V.i.e.n.n.a           A.u.s.t.r.i.a
e.m.a.i.l:        cstrato at aon.at
_._._._._._._._._._._._._._._._._._



On 9/2/13 2:44 PM, Scott Robinson [guest] wrote:
>
> 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
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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