chip removal from lumiBatch object
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Kilo Morkowi ▴ 10
@kilo-morkowi-6683
Last seen 8.4 years ago
Hi, I wil be very grateful if you could advise me on how can I correctly remove an outlier chip from llumiBatch object. For instance, let's assume that B01 sample in lumiBarnes example is an outlier. I'd like to remove it before normalization. How can this be done? Is here a method for deleting a chip? Many thanks for your help, --- Anastasia ps. I have imported data with lumiR function, added control info, modified phenoData, and made QC and plots.
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@james-w-macdonald-5106
Last seen 2 days ago
United States
Hi Anastasia, LumiBatch objects are direct extensions of the ExpressionSet class, so can be subsetted using the '[' operator: > smallLumi <- lumiBarnes[,-9] p> pData(phenoData(smallLumi)) sampleID label pctBlood pctPlacenta replicate A01 100USA A01 100 0 A A02 95US:5PA A02 95 5 A A03 75US:25PA A03 75 25 A A04 50US:50PA A04 50 50 A A05 25US:75PA A05 25 75 A A06 100PA A06 0 100 A A07 PBMC A07 NA NA A A08 Illumina Control A08 NA NA A B02 95US:5PB B02 95 5 B B03 75US:25PB B03 75 25 B B04 50US:50PB B04 50 50 B B05 25US:75PB B05 25 75 B B06 100PB B06 0 100 B B07 PaxGene B07 NA NA B B08 Illumina Control B08 NA NA B So you can see I removed the B01 sample. Best, Jim On 7/31/2014 6:09 PM, Kilo Morkowi wrote: > Hi, > > I wil be very grateful if you could advise me on how can I correctly remove an outlier chip from llumiBatch object. > > For instance, let's assume that B01 sample in lumiBarnes example is an outlier. I'd like to remove it before normalization. > > How can this be done? Is here a method for deleting a chip? > > Many thanks for your help, > --- Anastasia > > ps. > I have imported data with lumiR function, added control info, modified phenoData, and made QC and plots. > > _______________________________________________ > 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 > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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When I last worked with LumiBatch objects, I found that the [, -9] method did not subset control probes data. I'm pasting a work-around I used - apologies to maintainers that I didn't think at the time to report this. lumi.subset <- function(lumibatch.obj,index){ ##-------------------------------------------------------------------- ------ ##-------------------------------------------------------------------- ------ ## a work-around for a shortcoming in the lumibatch object, which does ## not subset control data when subsetting the object. ##-------------------------------------------------------------------- ------ ##lumibatch.obj: a lumibatch object to be subsetted ##index: an integer or logical vector specifying which samples to extract ## from the lumibatch object ##-------------------------------------------------------------------- ------ ##-------------------------------------------------------------------- ------ if(!(class(index)=="integer" | class(index)=="logical")){ error("index must be of type integer or logical") } ##temporarily set warn=-1 to suppress the warning you get when ##indexing a lumibatch object, since this function is a workaround ##to that limitation. options(warn=-1) lumibatch.reduced <- lumibatch.obj[,index] options(warn=0) controls.all <- getControlData(lumibatch.obj) controls <- controls.all[,c(match(c("controlType","ProbeID",sampleNames(lumibatch. reduced)),colnames(controls.all)))] if(all.equal(sampleNames(lumibatch.reduced),colnames(controls)[-1:-2 ])){ lumibatch.reduced <- addControlData2lumi(controls,lumibatch.reduced) print("Control data was correctly subsetted and inserted into the new lumibatch object.") }else{ error("couldn't match control data with reduced lumibatch object") } return(lumibatch.reduced) } On Fri, Aug 1, 2014 at 10:42 AM, James W. MacDonald <jmacdon@uw.edu> wrote: > Hi Anastasia, > > LumiBatch objects are direct extensions of the ExpressionSet class, so can > be subsetted using the '[' operator: > > > smallLumi <- lumiBarnes[,-9] > p> pData(phenoData(smallLumi)) > sampleID label pctBlood pctPlacenta replicate > A01 100USA A01 100 0 A > A02 95US:5PA A02 95 5 A > A03 75US:25PA A03 75 25 A > A04 50US:50PA A04 50 50 A > A05 25US:75PA A05 25 75 A > A06 100PA A06 0 100 A > A07 PBMC A07 NA NA A > A08 Illumina Control A08 NA NA A > B02 95US:5PB B02 95 5 B > B03 75US:25PB B03 75 25 B > B04 50US:50PB B04 50 50 B > B05 25US:75PB B05 25 75 B > B06 100PB B06 0 100 B > B07 PaxGene B07 NA NA B > B08 Illumina Control B08 NA NA B > > So you can see I removed the B01 sample. > > Best, > > Jim > > > > > On 7/31/2014 6:09 PM, Kilo Morkowi wrote: > >> Hi, >> >> I wil be very grateful if you could advise me on how can I correctly >> remove an outlier chip from llumiBatch object. >> >> For instance, let's assume that B01 sample in lumiBarnes example is an >> outlier. I'd like to remove it before normalization. >> >> How can this be done? Is here a method for deleting a chip? >> >> Many thanks for your help, >> --- Anastasia >> >> ps. >> I have imported data with lumiR function, added control info, modified >> phenoData, and made QC and plots. >> >> _______________________________________________ >> 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 >> >> > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > > _______________________________________________ > 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 > -- Levi Waldron Assistant Professor of Biostatistics City University of New York School of Public Health, Hunter College 2180 3rd Ave Rm 538 New York NY 10035-4003 phone: 212-396-7747 www.waldronlab.org [[alternative HTML version deleted]]
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