hi, I am working on two color 4x44Agilent array.I normalized the data with Bioconductor,I used the following scripts to normalize the data.i want to filterout the spots which are not good to be analysis across the array.how can i filter the spots which are having the negative value after background substraction.I want to do this befor normalization. >limma(library) > library(limma) > targets_nod=readTargets("Both_negatv_postv_nods.txt") > targets_nod SampleNumber FileName Cy3 Cy5 1 1 135kt_251485025987_1_4.txt normal tumor 2 2 157kt_251485025985_1_3.txt normal tumor 3 3 159kt_251485025985_1_4.txt normal tumor 4 4 171kt_251485026134_1_3.txt normal tumor 5 5 179kt_251485026134_1_4.txt normal tumor 6 6 28kt_251485025987_1_1.txt normal tumor 7 7 58kt_251485025986_1_1.txt normal tumor > RG<-read.maimages(targets_nod$FileName, source="agilent") > RG<-backgroundCorrect (RG,method="none") > MA<-normalizeWithinArrays(RG, method="loess") > MA <- normalizeBetweenArrays(RG, method="quantile") thank you, Neeraj Rana IISC Banglore,INDIA. [[alternative HTML version deleted]]

On Mon, Jan 18, 2010 at 11:26 PM, neeraj rana <kushrn at="" gmail.com=""> wrote: > hi, > > ? ? I am working on two color 4x44Agilent array.I normalized the data with > Bioconductor,I used the following scripts to normalize the data.i want to > filterout the spots which are not good to be analysis across the array.how > can i filter the spots which are having the negative value after background > substraction.I want to do this befor normalization. > >>limma(library) >> library(limma) >> targets_nod=readTargets("Both_negatv_postv_nods.txt") >> targets_nod > ? SampleNumber ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?FileName ? ?Cy3 > Cy5 > 1 ? ? ? ? ? ? 1 ? ? ? ? ? ? ? ? ? ? ? ?135kt_251485025987_1_4.txt normal > tumor > 2 ? ? ? ? ? ? 2 ? ? ? ? ? ? ? ? ? ? ? ?157kt_251485025985_1_3.txt normal > tumor > 3 ? ? ? ? ? ? 3 ? ? ? ? ? ? ? ? ? ? ? ?159kt_251485025985_1_4.txt normal > tumor > 4 ? ? ? ? ? ? 4 ? ? ? ? ? ? ? ? ? ? ? ?171kt_251485026134_1_3.txt normal > tumor > 5 ? ? ? ? ? ? 5 ? ? ? ? ? ? ? ? ? ? ? ?179kt_251485026134_1_4.txt normal > tumor > 6 ? ? ? ? ? ? 6 ? ? ? ? ? ? ? ? ? ? ? ? 28kt_251485025987_1_1.txt normal > tumor > 7 ? ? ? ? ? ? 7 ? ? ? ? ? ? ? ? ? ? ? ? 58kt_251485025986_1_1.txt normal > tumor >> RG<-read.maimages(targets_nod$FileName, source="agilent") Hi, Neeraj. RG is an RGList object and can be subset just like a normal data.frame or matrix (samples are columns, genes are rows). RG$G contains the Green intensities while RG$R contains the Red intensities. Sean >> RG<-backgroundCorrect (RG,method="none") >> MA<-normalizeWithinArrays(RG, method="loess") >> MA <- normalizeBetweenArrays(RG, method="quantile") > > thank you, > Neeraj Rana > IISC Banglore,INDIA. > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > 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 >

On Wed, Jan 20, 2010 at 12:12 AM, neeraj rana <kushrn at="" gmail.com=""> wrote: > hi thanx sean, > ???????? In RG list after background correction i shall get the R and G with > background corrected valves.I want to use subtract method to subtract the > background intensities from the forground intensities.And then i want to > remove the spots from the RG List which are not well above the background > intensities. Sounds like a plan. Let us know if you have questions. Sean > > On Tue, Jan 19, 2010 at 3:52 PM, Sean Davis <seandavi at="" gmail.com=""> wrote: >> >> On Mon, Jan 18, 2010 at 11:26 PM, neeraj rana <kushrn at="" gmail.com=""> wrote: >> > hi, >> > >> > ? ? I am working on two color 4x44Agilent array.I normalized the data >> > with >> > Bioconductor,I used the following scripts to normalize the data.i want >> > to >> > filterout the spots which are not good to be analysis across the >> > array.how >> > can i filter the spots which are having the negative value after >> > background >> > substraction.I want to do this befor normalization. >> > >> >>limma(library) >> >> library(limma) >> >> targets_nod=readTargets("Both_negatv_postv_nods.txt") >> >> targets_nod >> > ? SampleNumber ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?FileName ? ?Cy3 >> > Cy5 >> > 1 ? ? ? ? ? ? 1 ? ? ? ? ? ? ? ? ? ? ? ?135kt_251485025987_1_4.txt normal >> > tumor >> > 2 ? ? ? ? ? ? 2 ? ? ? ? ? ? ? ? ? ? ? ?157kt_251485025985_1_3.txt normal >> > tumor >> > 3 ? ? ? ? ? ? 3 ? ? ? ? ? ? ? ? ? ? ? ?159kt_251485025985_1_4.txt normal >> > tumor >> > 4 ? ? ? ? ? ? 4 ? ? ? ? ? ? ? ? ? ? ? ?171kt_251485026134_1_3.txt normal >> > tumor >> > 5 ? ? ? ? ? ? 5 ? ? ? ? ? ? ? ? ? ? ? ?179kt_251485026134_1_4.txt normal >> > tumor >> > 6 ? ? ? ? ? ? 6 ? ? ? ? ? ? ? ? ? ? ? ? 28kt_251485025987_1_1.txt normal >> > tumor >> > 7 ? ? ? ? ? ? 7 ? ? ? ? ? ? ? ? ? ? ? ? 58kt_251485025986_1_1.txt normal >> > tumor >> >> RG<-read.maimages(targets_nod$FileName, source="agilent") >> >> Hi, Neeraj. >> >> RG is an RGList object and can be subset just like a normal data.frame >> or matrix (samples are columns, genes are rows). ?RG$G contains the >> Green intensities while RG$R contains the Red intensities. >> >> Sean >> >> >> RG<-backgroundCorrect (RG,method="none") >> >> MA<-normalizeWithinArrays(RG, method="loess") >> >> MA <- normalizeBetweenArrays(RG, method="quantile") >> > >> > thank you, >> > Neeraj Rana >> > IISC Banglore,INDIA. >> > >> > ? ? ? ?[[alternative HTML version deleted]] >> > >> > _______________________________________________ >> > 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 >> > > >