GSE normalization
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Steve Taylor ▴ 100
@steve-taylor-1523
Last seen 10.2 years ago
Hi, I have created 3 separate GSE Objects, read from SOFT format files using GeoQuery. I would like to normalise across experiments using rma. What's the best way to merge the data and then normalise? Ultimately I want to analyse these using limma. Thanks for any help, Steve
limma GEOquery limma GEOquery • 1.9k views
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Weiwei Shi ★ 1.2k
@weiwei-shi-1407
Last seen 10.2 years ago
hi, Steve: I posted a similiar question as you yesterday and my situation is a little bit different from you: I have two ideas and one of them is to evaluae the variance across sites so normalization should not be done for that purpose; but my second idea needs the normalization, and my way of doing that is pool the CEL files in one directory and run justGCRMA or whatever on them. I am working on this approach now. Maybe we (or anyone interested in this) could share the experience. HTH, Weiwei On 6/22/07, Steve Taylor <staylor at="" molbiol.ox.ac.uk=""> wrote: > Hi, > > I have created 3 separate GSE Objects, read from SOFT format files using GeoQuery. I would like to normalise across experiments using rma. What's the best way to merge the data and then normalise? > Ultimately I want to analyse these using limma. > > Thanks for any help, > > Steve > > _______________________________________________ > 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 > -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed..." ---Matrix III
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Hi, > I posted a similiar question as you yesterday and my situation is a > little bit different from you: > I have two ideas and one of them is to evaluae the variance across > sites so normalization should not be done for that purpose; but my > second idea needs the normalization, and my way of doing that is pool > the CEL files in one directory and run justGCRMA or whatever on them. > I am working on this approach now. Maybe we (or anyone interested in > this) could share the experience. > Someone has just advised me (off list) that the SOFT files can't be analysed using rma since the data is at the gene level. So I guess downloading the CEL files is the best approach... Ultimately I would like to incorporate other platform(s) as well, though I realise this has many problems. Another set of data I have is from Functional ID v2.0 Array 1 from Rosetta, which I am not familiar with. Does anyone know what is the best normalisation procedure for this type of data? I agree with Weiwei though it would be useful to find out what is an appropriate methodology. I have had a brief look around and seen a bioconductor package called MergeMaid. Has anyone had any experience with this or can recommend something else? Thanks again, Steve > HTH, > > Weiwei > > On 6/22/07, Steve Taylor <staylor at="" molbiol.ox.ac.uk=""> wrote: > >> Hi, >> >> I have created 3 separate GSE Objects, read from SOFT format files >> using GeoQuery. I would like to normalise across experiments using >> rma. What's the best way to merge the data and then normalise? >> Ultimately I want to analyse these using limma. >> >> Thanks for any help, >> >> Steve >> >> _______________________________________________ >> 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 >> > >
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hi, Steve: if you look at my previous question, it has been suggested that pooling data might not be a good solution. -w On 6/22/07, Stephen Taylor <staylor at="" molbiol.ox.ac.uk=""> wrote: > Hi, > > > I posted a similiar question as you yesterday and my situation is a > > little bit different from you: > > I have two ideas and one of them is to evaluae the variance across > > sites so normalization should not be done for that purpose; but my > > second idea needs the normalization, and my way of doing that is pool > > the CEL files in one directory and run justGCRMA or whatever on them. > > I am working on this approach now. Maybe we (or anyone interested in > > this) could share the experience. > > > > Someone has just advised me (off list) that the SOFT files can't be > analysed using rma since the data is at the gene level. So I guess > downloading the CEL files is the best approach... > > Ultimately I would like to incorporate other platform(s) as well, though > I realise this has many problems. Another set of data I have is from > Functional ID v2.0 Array 1 from Rosetta, which I am not familiar with. > Does anyone know what is the best normalisation procedure for this type > of data? > > I agree with Weiwei though it would be useful to find out what is an > appropriate methodology. I have had a brief look around and seen a > bioconductor package called MergeMaid. Has anyone had any experience > with this or can recommend something else? > > Thanks again, > > Steve > > > HTH, > > > > Weiwei > > > > On 6/22/07, Steve Taylor <staylor at="" molbiol.ox.ac.uk=""> wrote: > > > >> Hi, > >> > >> I have created 3 separate GSE Objects, read from SOFT format files > >> using GeoQuery. I would like to normalise across experiments using > >> rma. What's the best way to merge the data and then normalise? > >> Ultimately I want to analyse these using limma. > >> > >> Thanks for any help, > >> > >> Steve > >> > >> _______________________________________________ > >> 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 > >> > > > > > > -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed..." ---Matrix III
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Hi Weiwei and steve, Go to this link: http://www.biostat.harvard.edu/~wjohnson/ComBat/. I tested this program, it worked fine for me. I don't have time to go through this paper, but it maybe give you some idea. Ruimin -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Weiwei Shi Sent: Friday, June 22, 2007 10:05 AM To: Stephen Taylor Cc: Bioconductor Subject: Re: [BioC] GSE normalization hi, Steve: if you look at my previous question, it has been suggested that pooling data might not be a good solution. -w On 6/22/07, Stephen Taylor <staylor at="" molbiol.ox.ac.uk=""> wrote: > Hi, > > > I posted a similiar question as you yesterday and my situation is a > > little bit different from you: > > I have two ideas and one of them is to evaluae the variance across > > sites so normalization should not be done for that purpose; but my > > second idea needs the normalization, and my way of doing that is > > pool the CEL files in one directory and run justGCRMA or whatever on them. > > I am working on this approach now. Maybe we (or anyone interested in > > this) could share the experience. > > > > Someone has just advised me (off list) that the SOFT files can't be > analysed using rma since the data is at the gene level. So I guess > downloading the CEL files is the best approach... > > Ultimately I would like to incorporate other platform(s) as well, > though I realise this has many problems. Another set of data I have is > from Functional ID v2.0 Array 1 from Rosetta, which I am not familiar with. > Does anyone know what is the best normalisation procedure for this > type of data? > > I agree with Weiwei though it would be useful to find out what is an > appropriate methodology. I have had a brief look around and seen a > bioconductor package called MergeMaid. Has anyone had any experience > with this or can recommend something else? > > Thanks again, > > Steve > > > HTH, > > > > Weiwei > > > > On 6/22/07, Steve Taylor <staylor at="" molbiol.ox.ac.uk=""> wrote: > > > >> Hi, > >> > >> I have created 3 separate GSE Objects, read from SOFT format files > >> using GeoQuery. I would like to normalise across experiments using > >> rma. What's the best way to merge the data and then normalise? > >> Ultimately I want to analyse these using limma. > >> > >> Thanks for any help, > >> > >> Steve > >> > >> _______________________________________________ > >> 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 > >> > > > > > > -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed..." ---Matrix III _______________________________________________ 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
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