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

Fri Oct 11 19:10:08 CEST 2013

Dear All,

Sorry about the delay, I was given other priorities and am just getting back to this. I read the tutorial and the paper on that harshlight package and it looks good. Can anyone think of a reason that it only has 19 citations on pubmed despite being published back in 2005? 

Is it simply that because of the random spatial distribution of probes (Christian mentioned) and the robustness of gcrma (as shown in the harshlight paper itself) people do not deem it worth doing? Is there any reason to not do it, when it would make the stats a little cleaner?

Thanks,

Scott

________________________________________
From: Mark Dunning [mark.dunning at gmail.com]
Sent: 02 September 2013 18:20
To: Scott Robinson
Cc: cstrato; bioconductor at r-project.org
Subject: Re: [BioC] How does one deal with spatial effects detected on single channel microarrays?

I believe that the Harshlight package deals with spatial artefacts on affy chips

Mark

On Mon, Sep 2, 2013 at 6:18 PM, Scott Robinson <Scott.Robinson at glasgow.ac.uk<mailto:Scott.Robinson at glasgow.ac.uk>> wrote:
Dear Christian,

Brilliant, thanks very much. I have just one last query: if I were to have a more detrimental spatial effect do you (or anyone) know what BioC package (if any exists) would be appropriate for spatial normalization of single-channel Affy chips? Or is it simply a case of removing that sample?

Many thanks,

Scott

PS I posted this same question a week or two ago on biostars.org<http://biostars.org> but got no answers. I hope you wouldn't mind if I formulate an 'answer' out of what you have said to post on biostars, and accrediting you?

-----Original Message-----
From: cstrato [mailto:cstrato at aon.at<mailto:cstrato at aon.at>]
Sent: 02 September 2013 18:09
To: Scott Robinson
Cc: Scott Robinson [guest]; bioconductor at r-project.org<mailto:bioconductor at r-project.org>
Subject: Re: [BioC] How does one deal with spatial effects detected on single channel microarrays?

Dear Scott,

Yes and yes, however even the crop circles may be ok. There are a lot of quality controls that you can do additionally, e.g. PCA, NUSE, RLE, border plots, center of intensity plots, etc.

Best regards,
Christian

On 9/2/13 6:41 PM, Scott Robinson wrote:
> 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<mailto:cstrato at aon.at>]
> Sent: 02 September 2013 16:28
> To: Scott Robinson [guest]
> Cc: bioconductor at r-project.org<mailto: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<http://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<http://bioconductor.org>.
>>
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