RMA in Bioconductor versus APT

RMA in Bioconductor versus APT - missing probesets

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Michal Blazejczyk ▴ 320

@michal-blazejczyk-2231

Last seen 10.3 years ago

Dear group, I have noticed that Bioconductor's just.rma() function returns fewer transcript-level probesets that RMA in APT for the Human Gene 1.0 ST array. To be specific, 819 probesets are missing, and most of them seem to be "real", i.e. they are annotated when I run them through NetAffx. I would like to know why this is happening, and whether it is to be expected or maybe it is a bug. Best regards, Micha? B?a?ejczyk FlexArray Lead Developer McGill University and Genome Quebec Innovation Centre http://www.gqinnovationcenter.com/services/bioinformatics/flexarray/in dex.aspx?l=e

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ADD COMMENT • link updated 13.8 years ago by cstrato ★ 3.9k • written 13.8 years ago by Michal Blazejczyk ▴ 320

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Guido Hooiveld ★ 4.1k

@guido-hooiveld-2020

Last seen 5 days ago

Wageningen University, Wageningen, the …

Hi, I think this is to be expected. I assume [since you did not included your sessionInfo()] you used the CDF environment that has been made form the *unsupported* CDF file Affymetrix provides. This unsupported CDF was generated by Affymetrix back in early 2007, and since then the annotation hence probeset definitions have been updated (hg18 vs hg19), which may explain part of your observation. Also, at a certain moment Affymetrix decided to remove (ignore) probesets consisting of less than 4 probes. See e.g. this post: http://article.gmane.org/gmane.science.biology.informatics.conductor/2 0999 that mentions this for the mouse Gene ST array. HTH, Guido ------------------------------------------------ Guido Hooiveld, PhD Nutrition, Metabolism & Genomics Group Division of Human Nutrition Wageningen University Biotechnion, Bomenweg 2 NL-6703 HD Wageningen the Netherlands tel: (+)31 317 485788 fax: (+)31 317 483342 email:????? guido.hooiveld at wur.nl internet:?? http://nutrigene.4t.com http://www.researcherid.com/rid/F-4912-2010 -----Original Message----- From: bioconductor-bounces@r-project.org [mailto:bioconductor- bounces@r-project.org] On Behalf Of Michal Blazejczyk Sent: Wednesday, February 23, 2011 19:07 To: bioconductor at r-project.org Subject: [BioC] RMA in Bioconductor versus APT - missing probesets Dear group, I have noticed that Bioconductor's just.rma() function returns fewer transcript-level probesets that RMA in APT for the Human Gene 1.0 ST array. To be specific, 819 probesets are missing, and most of them seem to be "real", i.e. they are annotated when I run them through NetAffx. I would like to know why this is happening, and whether it is to be expected or maybe it is a bug. Best regards, Micha? B?a?ejczyk FlexArray Lead Developer McGill University and Genome Quebec Innovation Centre http://www.gqinn ovationcenter.com/services/bioinformatics/flexarray/index.aspx?l=e _______________________________________________ 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

ADD COMMENT • link 13.8 years ago Guido Hooiveld ★ 4.1k

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cstrato ★ 3.9k

@cstrato-908

Last seen 6.2 years ago

Austria

Dear Michal, As an alternative to just.rma() you could use the Bioconductor package xps which uses the Affymetrix PGF-file as well as the Affymetrix annotations, and thus should contain all probesets. xps has also a vignette, "APTvsXPS.pdf" which compares the results for RMA obtained from APT vs xps, respectively, for the HuGene 1.0 ST array. 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 2/23/11 7:06 PM, Michal Blazejczyk wrote: > Dear group, > > I have noticed that Bioconductor's just.rma() function returns fewer transcript-level > probesets that RMA in APT for the Human Gene 1.0 ST array. To be specific, 819 probesets > are missing, and most of them seem to be "real", i.e. they are annotated when I run them > through NetAffx. > > I would like to know why this is happening, and whether it is to be expected or maybe > it is a bug. > > Best regards, > > Micha? B?a?ejczyk > FlexArray Lead Developer > McGill University and Genome Quebec Innovation Centre > http://www.gqinnovationcenter.com/services/bioinformatics/flexarray/ index.aspx?l=e > > _______________________________________________ > 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

ADD COMMENT • link 13.8 years ago cstrato ★ 3.9k

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Dear Christian, I am aware of the existence of xps. However, we can't use it for our purposes, largely because it is too complicated to set up (or at least, that was the case the last time we looked at it). I would still like to know what's happening in just.rma() :) Best, Micha? cstrato <cstrato at="" aon.at=""> wrote: > Dear Michal, > As an alternative to just.rma() you could use the Bioconductor package > xps which uses the Affymetrix PGF-file as well as the Affymetrix > annotations, and thus should contain all probesets. xps has also a > vignette, "APTvsXPS.pdf" which compares the results for RMA obtained > from APT vs xps, respectively, for the HuGene 1.0 ST array. > 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 2/23/11 7:06 PM, Michal Blazejczyk wrote: >> Dear group, >> >> I have noticed that Bioconductor's just.rma() function returns fewer transcript-level >> probesets that RMA in APT for the Human Gene 1.0 ST array. To be specific, 819 probesets >> are missing, and most of them seem to be "real", i.e. they are annotated when I run them >> through NetAffx. >> >> I would like to know why this is happening, and whether it is to be expected or maybe >> it is a bug. >> >> Best regards, >> >> Micha? B?a?ejczyk >> FlexArray Lead Developer >> McGill University and Genome Quebec Innovation Centre >> http://www.gqinnovationcenter.com/services/bioinformatics/flexarray /index.aspx?l=e >> >> _______________________________________________ >> 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

ADD REPLY • link 13.8 years ago Michal Blazejczyk ▴ 320

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Dear Michal,, Did you check the README file coming with xps which explains how to set it up? Furthermore, feel free to send me an email if you have any problems, I will try to help you the best I can. Best regards Christian On 2/23/11 10:40 PM, Michal Blazejczyk wrote: > Dear Christian, > > I am aware of the existence of xps. However, we can't use it for our purposes, > largely because it is too complicated to set up (or at least, that was the case > the last time we looked at it). I would still like to know what's happening in > just.rma() :) > > Best, > Micha? > > > > cstrato<cstrato at="" aon.at=""> wrote: >> Dear Michal, > >> As an alternative to just.rma() you could use the Bioconductor package >> xps which uses the Affymetrix PGF-file as well as the Affymetrix >> annotations, and thus should contain all probesets. xps has also a >> vignette, "APTvsXPS.pdf" which compares the results for RMA obtained >> from APT vs xps, respectively, for the HuGene 1.0 ST array. > >> 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 2/23/11 7:06 PM, Michal Blazejczyk wrote: >>> Dear group, >>> >>> I have noticed that Bioconductor's just.rma() function returns fewer transcript-level >>> probesets that RMA in APT for the Human Gene 1.0 ST array. To be specific, 819 probesets >>> are missing, and most of them seem to be "real", i.e. they are annotated when I run them >>> through NetAffx. >>> >>> I would like to know why this is happening, and whether it is to be expected or maybe >>> it is a bug. >>> >>> Best regards, >>> >>> Micha? B?a?ejczyk >>> FlexArray Lead Developer >>> McGill University and Genome Quebec Innovation Centre >>> http://www.gqinnovationcenter.com/services/bioinformatics/flexarra y/index.aspx?l=e >>> >>> _______________________________________________ >>> 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 > >

ADD REPLY • link 13.8 years ago cstrato ★ 3.9k

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