Dear Lana, Maybe you could use package xps, which I have updated to work with miRNAs, see: https://www.stat.math.ethz.ch/pipermail/bioconductor/2009-August/02914 4.html In case you have a custom CDF for the human miRNAs only you could in principle use this CDF file. 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 _._._._._._._._._._._._._._._._._._ Lana Schaffer wrote: > James and all, > I have asked Affymetrix to create a CDF for the human species on the miRNA chip. > They have created this type of CDF for our custom arrays which we use all the time. > Lana > > ________________________________________ > From: James W. MacDonald [jmacdon at med.umich.edu] > Sent: Thursday, October 15, 2009 11:57 AM > To: Chao-Jen Wong > Cc: Lana Schaffer; bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] Affy miRNA > > For what it's worth, I just built a cdf and probe package for the Affy > miRNA chip that will be part of BioC2.5, and which should allow one to > use the affy pipeline to analyze these data. > > That said, I highly doubt the canonical affy analysis (e.g., ReadAffy(), > rma()) will be a reasonable thing to do, as this chip contains miRNA > from 71 different species. I would imagine one would want to subset out > those probesets that pertained to the species at hand before proceeding > with analysis, and that is a non-trivial exercise. > > This post to the BioC listserv by Jenny Drnevich should be quite helpful > in that endeavor: > > http://article.gmane.org/gmane.science.biology.informatics.conductor /19867/match=affybatch+probe > > Best, > > Jim > > > > Chao-Jen Wong wrote: > >> Hi, Lana >> >> As far as I know, Bioconductor does not have a package for Affy miRNA >> chip yet. There is a package for Agilent miRNA chips (available from >> BioC 2.5) using rma for normalization. I would also be interested in >> any suggestions for nomarlization for Affy miRNA chips. >> >> Thanks, >> Chao-Jen >> >> Lana Schaffer wrote: >> >>> Hi, >>> Is there Bioconductor software for the new Affy miRNA chip? >>> Does someone have experience normalizing the Affy miRNA chip? >>> Any suggestions? >>> >>> Lana Schaffer >>> Biostatistics/Informatics >>> The Scripps Research Institute >>> DNA Array Core Facility >>> La Jolla, CA 92037 >>> (858) 784-2263 >>> (858) 784-2994 >>> schaffer at scripps.edu >>> >>> _______________________________________________ >>> 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 >>> >>> >> > > -- > James W. MacDonald, M.S. > Biostatistician > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > > _______________________________________________ > 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 > >

All, Dr. de Groot has given me this link for CDF and annotation files: http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/12. 0.0/mirbaseg.asp I would like to note here that Agilent arrays contain >4 arrays on one chip, so the normalization may not need to be so stringent as with the single Affymetrix arrays. I have successfully used Agilant-MAD scaled normalizeBetweenArrays(x,method="scale") previously for Agilant data. Perhaps this will also work for the Affymetrix chips? Lana -----Original Message----- From: Hooiveld, Guido [mailto:Guido.Hooiveld@wur.nl] Sent: Thursday, October 15, 2009 1:12 PM To: James W. MacDonald; Chao-Jen Wong Cc: Lana Schaffer; bioconductor at stat.math.ethz.ch Subject: RE: [BioC] Affy miRNA To follow up op on this: I also just got the data of my miRNA profiling experiment performed on Affy arrays. Upon request Manhong Dai and Fan Meng at the MBNI were so kind to 'remap' the miRNA probes last August to mirBASE version 13, both to genome loaction and fasta files, for human, mouse and rat. Please find the links below. Also note that last september mirBASE updated to version 14, so the remapping *might* not completely up to date (although I don't think human/mouse/rat are seriously affected). With these custom CDF it should be possible to read the data using ReadAffy(). Currently I am evaluating which normalization strategy would be best for these relatively small number of probesets. RMA may indeed be an good option, but I have read before on this list that VSN may also be a good normalization method (in the the discussion regarding the Agilent miRNA array [1-color]). http://article.gmane.org/gmane.science.biology.informatics.conductor/1 40 96 Regards, Guido ---------------------------------------------------------------------- -- -------- From: Manhong Dai Sent: Fri 21-8-2009 16:22 To: Groot, Philip de Cc: Hooiveld, Guido; Meng Fan Subject: mirbase custom CDF Hi, mirbase custom CDF is generated. http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/12. 0. 0/mirbaseg.asp is based on genome location, the files we used can be got by searching 'miRNAgff' in http://brainarray.mbni.med.umich.edu/Br ainarray/Database/CustomCDF/12.0. 0/version.html http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/12. 0. 0/mirbasef.asp is based on mirbase fasta files, which are the bottom three lines of http://brainarray.mbni.med.umich.edu/Brainarray/Databas e/CustomCDF/12.0. 0/version.html Please let me know if you came across any problem. Best, Manhong ------------------------------------------------ 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 internet: http://nutrigene.4t.com email: guido.hooiveld at wur.nl > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of James W. > MacDonald > Sent: 15 October 2009 20:57 > To: Chao-Jen Wong > Cc: Lana Schaffer; bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] Affy miRNA > > For what it's worth, I just built a cdf and probe package for the Affy > miRNA chip that will be part of BioC2.5, and which should allow one to > use the affy pipeline to analyze these data. > > That said, I highly doubt the canonical affy analysis (e.g., > ReadAffy(), > rma()) will be a reasonable thing to do, as this chip contains miRNA > from 71 different species. I would imagine one would want to subset > out those probesets that pertained to the species at hand before > proceeding with analysis, and that is a non-trivial exercise. > > This post to the BioC listserv by Jenny Drnevich should be quite > helpful in that endeavor: > > http://article.gmane.org/gmane.science.biology.informatics.con > ductor/19867/match=affybatch+probe > > Best, > > Jim > > > > Chao-Jen Wong wrote: > > Hi, Lana > > > > As far as I know, Bioconductor does not have a package for > Affy miRNA > > chip yet. There is a package for Agilent miRNA chips > (available from > > BioC 2.5) using rma for normalization. I would also be > interested in > > any suggestions for nomarlization for Affy miRNA chips. > > > > Thanks, > > Chao-Jen > > > > Lana Schaffer wrote: > >> Hi, > >> Is there Bioconductor software for the new Affy miRNA chip? > >> Does someone have experience normalizing the Affy miRNA chip? > >> Any suggestions? > >> > >> Lana Schaffer > >> Biostatistics/Informatics > >> The Scripps Research Institute > >> DNA Array Core Facility > >> La Jolla, CA 92037 > >> (858) 784-2263 > >> (858) 784-2994 > >> schaffer at scripps.edu > >> > >> _______________________________________________ > >> 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 > >> > > > > > > -- > James W. MacDonald, M.S. > Biostatistician > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > > _______________________________________________ > 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 > >

Rao and collaborators have looked at different methods. A Comparison of Normalization Techniques for MicroRNA Microarray Data http://www.bepress.com/sagmb/vol7/iss1/art22/ L. PS: quantile-based normalization is one step in RMA. I am not sure that the probe summarization method applies for miRNA (worth a look, but those a likely very short - I do not how many probes per miRNA are on the affy chip) Hooiveld, Guido wrote: > To follow up op on this: > > I also just got the data of my miRNA profiling experiment performed on > Affy arrays. > Upon request Manhong Dai and Fan Meng at the MBNI were so kind to > 'remap' the miRNA probes last August to mirBASE version 13, both to > genome loaction and fasta files, for human, mouse and rat. Please find > the links below. Also note that last september mirBASE updated to > version 14, so the remapping *might* not completely up to date (although > I don't think human/mouse/rat are seriously affected). > > With these custom CDF it should be possible to read the data using > ReadAffy(). > Currently I am evaluating which normalization strategy would be best for > these relatively small number of probesets. RMA may indeed be an good > option, but I have read before on this list that VSN may also be a good > normalization method (in the the discussion regarding the Agilent miRNA > array [1-color]). > > http://article.gmane.org/gmane.science.biology.informatics.conductor /140 > 96 > > > Regards, > Guido > > > > -------------------------------------------------------------------- ---- > -------- > From: Manhong Dai > Sent: Fri 21-8-2009 16:22 > To: Groot, Philip de > Cc: Hooiveld, Guido; Meng Fan > Subject: mirbase custom CDF > > > Hi, > > > mirbase custom CDF is generated. > > http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/1 2.0. > 0/mirbaseg.asp is based on genome location, the files we used can be got > by searching 'miRNAgff' in > http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/1 2.0. > 0/version.html > > > http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/1 2.0. > 0/mirbasef.asp is based on mirbase fasta files, which are the bottom > three lines of > http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/1 2.0. > 0/version.html > > > > Please let me know if you came across any problem. > > > Best, > Manhong > > > > > > ------------------------------------------------ > 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 > internet: http://nutrigene.4t.com > email: guido.hooiveld at wur.nl > > > >> -----Original Message----- >> From: bioconductor-bounces at stat.math.ethz.ch >> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of >> James W. MacDonald >> Sent: 15 October 2009 20:57 >> To: Chao-Jen Wong >> Cc: Lana Schaffer; bioconductor at stat.math.ethz.ch >> Subject: Re: [BioC] Affy miRNA >> >> For what it's worth, I just built a cdf and probe package for >> the Affy miRNA chip that will be part of BioC2.5, and which >> should allow one to use the affy pipeline to analyze these data. >> >> That said, I highly doubt the canonical affy analysis (e.g., >> ReadAffy(), >> rma()) will be a reasonable thing to do, as this chip >> contains miRNA from 71 different species. I would imagine one >> would want to subset out those probesets that pertained to >> the species at hand before proceeding with analysis, and that >> is a non-trivial exercise. >> >> This post to the BioC listserv by Jenny Drnevich should be >> quite helpful in that endeavor: >> >> http://article.gmane.org/gmane.science.biology.informatics.con >> ductor/19867/match=affybatch+probe >> >> Best, >> >> Jim >> >> >> >> Chao-Jen Wong wrote: >>> Hi, Lana >>> >>> As far as I know, Bioconductor does not have a package for >> Affy miRNA >>> chip yet. There is a package for Agilent miRNA chips >> (available from >>> BioC 2.5) using rma for normalization. I would also be >> interested in >>> any suggestions for nomarlization for Affy miRNA chips. >>> >>> Thanks, >>> Chao-Jen >>> >>> Lana Schaffer wrote: >>>> Hi, >>>> Is there Bioconductor software for the new Affy miRNA chip? >>>> Does someone have experience normalizing the Affy miRNA chip? >>>> Any suggestions? >>>> >>>> Lana Schaffer >>>> Biostatistics/Informatics >>>> The Scripps Research Institute >>>> DNA Array Core Facility >>>> La Jolla, CA 92037 >>>> (858) 784-2263 >>>> (858) 784-2994 >>>> schaffer at scripps.edu >>>> >>>> _______________________________________________ >>>> 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 >>>> >>> >> -- >> James W. MacDonald, M.S. >> Biostatistician >> Douglas Lab >> University of Michigan >> Department of Human Genetics >> 5912 Buhl >> 1241 E. Catherine St. >> Ann Arbor MI 48109-5618 >> 734-615-7826 >> >> _______________________________________________ >> 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 >> >> > > _______________________________________________ > 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