Question: RMA normalisation of test microarray data to training data
0
gravatar for Daniel Brewer
7.6 years ago by
Daniel Brewer1.9k
Daniel Brewer1.9k wrote:
Hello, We have done some analysis on a set of Affy microarray data normalised by RMA and produced a predictor. We would like to test this predictor on a training set we have. Is it possible to RMA normalise the test dataset so that the probes have the same distribution as the training dataset without normalising all the data together? Our concern is that if you normalise them all together then this would mean we would have to go through all the analyses again. Thanks Dan -- ************************************************************** Daniel Brewer, Ph.D. Institute of Cancer Research Prostate Cancer Genome Team ************************************************************** The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the a...{{dropped:5}}
microarray go cancer affy • 573 views
ADD COMMENTlink modified 7.6 years ago by James W. MacDonald50k • written 7.6 years ago by Daniel Brewer1.9k
Answer: RMA normalisation of test microarray data to training data
0
gravatar for James W. MacDonald
7.6 years ago by
United States
James W. MacDonald50k wrote:
Hi Daniel, On 1/13/2012 8:47 AM, Daniel Brewer wrote: > Hello, > > We have done some analysis on a set of Affy microarray data normalised by RMA and produced a predictor. We would like to test this predictor on a training set we have. Is it possible to RMA normalise the test dataset so that the probes have the same distribution as the training dataset without normalising all the data together? Our concern is that if you normalise them all together then this would mean we would have to go through all the analyses again. If you had used the frma package for the initial processing, then yes. There may even be some way to use frma with your extant processed data, but you would have to look to see. Best, Jim > > Thanks > > Dan > -- 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 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
ADD COMMENTlink written 7.6 years ago by James W. MacDonald50k
If the interest is really at *normalization*: save the target distribution estimated from the training set, then use preprocessCore::normalize.quantiles.use.target. b On 13 January 2012 14:08, James W. MacDonald <jmacdon at="" med.umich.edu=""> wrote: > Hi Daniel, > > > On 1/13/2012 8:47 AM, Daniel Brewer wrote: >> >> Hello, >> >> We have done some analysis on a set of Affy microarray data normalised by >> RMA and produced a predictor. ?We would like to test this predictor on a >> training set we have. ?Is it possible to RMA normalise the test dataset so >> that the probes have the same distribution as the training dataset without >> normalising all the data together? ?Our concern is that if you normalise >> them all together then this would mean we would have to go through all the >> analyses again. > > > If you had used the frma package for the initial processing, then yes. There > may even be some way to use frma with your extant processed data, but you > would have to look to see. > > Best, > > Jim > > >> >> Thanks >> >> Dan >> > > -- > 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 > > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not be > used for urgent or sensitive issues > _______________________________________________ > 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 REPLYlink written 7.6 years ago by Benilton Carvalho4.3k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 339 users visited in the last hour