How does one deal with spatial effects detected on single channel microarrays?
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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.
Microarray Normalization affy marray nnNorm Microarray Normalization affy marray nnNorm • 1.6k views
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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 at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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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 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. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
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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] > 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. >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >
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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 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] > 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. >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >
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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]]
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Dear Scott, I forgot to mention one QC, namely the density plots of the raw data. If some of the mentioned QCs show that the corresponding CEL-file may have problems, I would simply remove it. Best regards, Christian On 9/2/13 7:18 PM, Scott Robinson 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 at aon.at] > Sent: 02 September 2013 18:09 > To: Scott Robinson > Cc: Scott Robinson [guest]; 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] >> 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. >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >
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