At 23:09 2004-02-18, you wrote: >Message: 8 >Date: Wed, 18 Feb 2004 16:25:36 -0600 >From: Joyce Gu <jwgu@bcm.tmc.edu> >Subject: [BioC] Mising data >To: bioconductor@stat.math.ethz.ch >Message-ID: <4033E6B9@webmail.bcm.tmc.edu> >Content-Type: text/plain; charset="ISO-8859-1" > >Hello, >I am using marrayInput packages to do my data analysis. After I read into my >data with read.marrayRaw function. I found that lots of my data is labelled >"NA". I use name.Gf="Ch1 Median",name.Rf="Ch2 Median",name.Gb=" Ch1 B >Median",name.Rb="Ch2 B Median" command, I am wondering how marrayClass >transformed data. Is still M vs A or what. >I want to normalize my data with this packages, then export to do further >analysis with other software. > >Any explanation is greatly appreciated about this algorithm > >Thanks > > > >------------------------------ Hi Joyce, First thing to do is to verify that your files are ok and that the variables names (e.g. " Ch1 B Median") matches exactly those within your files. You may start by reading in data from one of your files like for e.g.: fname<-"~/joyce/myfile.txt" Then to read the file with the read.table function like: data<- read.table(fname, header=TRUE, sep="\t", dec=".") Now see the names of variables in your file like names(data) You can check also the integrity your data looking at the values of "data" object. >>I am wondering how marrayClass transformed data. Is still M vs A or what. The object, (lets call it rawdata) of class marrayRaw that you obtain with read.marray function will contain in the slots maRf, maGf ...etc, exactly the same values you have in your files in the columns Ch2 Median, Ch1 Median ..etc, so they are not at all transformed. However, the A and M values (you may retrieve from the slots maA, and maM) are additional, being computed form maRf, maRb, maGf, maGb. >>I want to normalize my data with this packages For normalization you may use maNormMain function, after loading the marrayNorm library. You may have details on it with "? maNormMain". A print-tip loess normalization may be simply done like normdata<-maNormMain(rawdata, f.loc=list(maNormLoess() )) >> then export to do further analysis with other software You may retrieve any information from the nomalized object, normdata, using the appropriate methods of the class marrayNorm it belongs to. For eg maM(normdata) will give you a matrix with the normalized M values that you may further print into files with the "write.table" function for e.g. good luck, Laurentiu Tarca