Positive correlation between dye-swap technical replicates
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@philip-lijnzaad-2499
Last seen 2.2 years ago
European Union
> In limma manual it is written that correlation should be negative for > dye swaps- why is it positive?- is it a question of wrong model matrix > or is it something wrong with my samples? I concur with Juan Pedro that the most likely cause of this problem is mislabeling of the data; often they are already 'swapped back' for convenience, which is of course wrong. Regarding dye-bias, it would have be to really extreme to get the thing you're seeing. But more generally, if you are worried about gene-specific dyebias (and basically everyone should be), you could take a look at the dyebias package. It implements a method published recently by us (Margaritis et al., Mol. Sys. Biol. 2009, doi:10.1038/msb.2009.21). You can use the dyebias package to (1) recognize if there is any gene- specific dyebias; (2) which genes are affected most badly; (3) which slides are affected most badly; and (4) to correct it. Including a Dye effect in Limma is useful, but not enough: linear models cannot cope with the fact that the dye bias artefact depends not only on the gene, but also on the hybridization (for details, see the paper). The latter was not realized previously. We frequently achieve variance reductions of M of over 50%. The only prerequisite is a set of dye-swaps. If you run into difficulties using the package, please feel free to drop me a line. Regards, Philip -- Philip Lijnzaad, PhD Holstege Genomics Laboratory Dept. of Biomedical Genetics University Medical Center (UMC), Utrecht Stratenum room 2.211 (on Tuesdays and Thursdays not in after 15.00) MSN chat (*NOT* email): philip_lijnzaad at hotmail.com P.O. Box 85060, 3508 AB Utrecht (Universiteitsweg 100, 3584 CG Utrecht) The Netherlands tel: +31 (0)8875 68464 fax: +31 (0)8875 68479 ---------------------------------------------------------------------- -------- De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. ---------------------------------------------------------------------- -------- This message may contain confidential information and is...{{dropped:8}}
limma dyebias limma dyebias • 992 views
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Naomi Altman ★ 6.0k
@naomi-altman-380
Last seen 3.5 years ago
United States
I have seen positive correlation between dye-swaps due to dye degradation. --Naomi At 12:20 PM 2/3/2010, Philip Lijnzaad wrote: > > In limma manual it is written that correlation should be negative for > > dye swaps- why is it positive?- is it a question of wrong model matrix > > or is it something wrong with my samples? > >I concur with Juan Pedro that the most likely cause of this problem is >mislabeling of the data; often they are already 'swapped back' for >convenience, which is of course wrong. > >Regarding dye-bias, it would have be to really extreme to get the thing >you're seeing. > >But more generally, if you are worried about gene-specific dyebias (and >basically everyone should be), you could take a look at the dyebias package. >It implements a method published recently by us (Margaritis et al., Mol. Sys. >Biol. 2009, doi:10.1038/msb.2009.21). > >You can use the dyebias package to (1) recognize if there is any >gene-specific >dyebias; (2) which genes are affected most badly; (3) which slides are >affected most badly; and (4) to correct it. Including a Dye effect in Limma >is useful, but not enough: linear models cannot cope with the fact that the >dye bias artefact depends not only on the gene, but also on the hybridization >(for details, see the paper). The latter was not realized previously. > >We frequently achieve variance reductions of M of over 50%. The only >prerequisite is a set of dye-swaps. If you run into difficulties using the >package, please feel free to drop me a line. > >Regards, > > Philip > >-- >Philip Lijnzaad, PhD >Holstege Genomics Laboratory >Dept. of Biomedical Genetics >University Medical Center (UMC), Utrecht >Stratenum room 2.211 (on Tuesdays and Thursdays not in after 15.00) >MSN chat (*NOT* email): philip_lijnzaad at hotmail.com >P.O. Box 85060, 3508 AB Utrecht >(Universiteitsweg 100, 3584 CG Utrecht) >The Netherlands >tel: +31 (0)8875 68464 >fax: +31 (0)8875 68479 > >--------------------------------------------------------------------- --------- > >De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is >uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht >ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct >te informeren door het bericht te retourneren. Het Universitair Medisch >Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin >van de W.H.W. >(Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij >de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. > >Denk s.v.p aan het milieu voor u deze e-mail afdrukt. > >--------------------------------------------------------------------- --------- > >This message may contain confidential information and is...{{dropped:8}} > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor Naomi S. Altman 814-865-3791 (voice) Associate Professor Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111
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