Question: Normalizing a dataset from GEO to suit a classifier trained on another dataset
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6.3 years ago by
Guest User12k
Guest User12k wrote:
Hi, I have a built a classifier on a set of my own microarray data. I would like to be able to show that it works on new data, by taking some from GEO (same tissue, same array platform etc) and classifying that. However, the probe values in the new datasets are offset compared to those in my original dataset, presumably because of differences in how they were normalised. Is there a way to normalize datasets taken from GEO so that they are normalized with respect to an existing dataset? Thanks -- output of sessionInfo(): - -- Sent via the guest posting facility at bioconductor.org.
microarray probe • 511 views
ADD COMMENTlink modified 6.3 years ago by Matthew McCall830 • written 6.3 years ago by Guest User12k
Answer: Normalizing a dataset from GEO to suit a classifier trained on another dataset
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6.3 years ago by
United States
Matthew McCall830 wrote:
Nathan, Take a look at the frma package and paper: McCall MN, Bolstad BM, and Irizarry RA* (2010). Frozen Robust Multi-Array Analysis (fRMA), Biostatistics, 11(2):242-253. Best, Matt On Sun, Apr 14, 2013 at 10:40 AM, Nathan Skene [guest] <guest at="" bioconductor.org=""> wrote: > > Hi, > > I have a built a classifier on a set of my own microarray data. > > I would like to be able to show that it works on new data, by taking some from GEO (same tissue, same array platform etc) and classifying that. > > However, the probe values in the new datasets are offset compared to those in my original dataset, presumably because of differences in how they were normalised. > > Is there a way to normalize datasets taken from GEO so that they are normalized with respect to an existing dataset? > > Thanks > > > -- output of sessionInfo(): > > - > > -- > 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 -- Matthew N McCall, PhD 112 Arvine Heights Rochester, NY 14611 Cell: 202-222-5880
ADD COMMENTlink written 6.3 years ago by Matthew McCall830
Hi Matt, That looks like exactly the thing... but it wouldn't work on Illumina, right? RMA is Affy only? Thanks, Nathan On 14 April 2013 16:43, Matthew McCall <mccallm@gmail.com> wrote: > Nathan, > > Take a look at the frma package and paper: > McCall MN, Bolstad BM, and Irizarry RA* (2010). Frozen Robust > Multi-Array Analysis (fRMA), Biostatistics, 11(2):242-253. > > Best, > Matt > > > > On Sun, Apr 14, 2013 at 10:40 AM, Nathan Skene [guest] > <guest@bioconductor.org> wrote: > > > > Hi, > > > > I have a built a classifier on a set of my own microarray data. > > > > I would like to be able to show that it works on new data, by taking > some from GEO (same tissue, same array platform etc) and classifying that. > > > > However, the probe values in the new datasets are offset compared to > those in my original dataset, presumably because of differences in how they > were normalised. > > > > Is there a way to normalize datasets taken from GEO so that they are > normalized with respect to an existing dataset? > > > > Thanks > > > > > > -- output of sessionInfo(): > > > > - > > > > -- > > 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 > > > > -- > Matthew N McCall, PhD > 112 Arvine Heights > Rochester, NY 14611 > Cell: 202-222-5880 > [[alternative HTML version deleted]]
ADD REPLYlink written 6.3 years ago by natske10
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