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@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 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@aon.at]
> Sent: 02 September 2013 18:09
> To: Scott Robinson
> Cc: Scott Robinson [guest]; bioconductor@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@aon.at]
> > Sent: 02 September 2013 16:28
> > To: Scott Robinson [guest]
> > Cc: bioconductor@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.
> >>
> >> _______________________________________________
> >> Bioconductor mailing list
> >> Bioconductor@r-project.org
> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> Search the archives:
> >> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>
> >
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>

	[[alternative HTML version deleted]]

