Dear All, I am working with 13 different data sets (containing 550 arrays in total) which is normalized using general linear model for print-tip. I am trying to do following: 1) Merging all 13 different data sets: To merge these data sets I built ExpressionSet for each data set. Then I made a list of these ExpressionSets and named it "fullset1". Then to merge red and green intensity I did following: red1 = lapply(fullset1,function(eset) exprs(eset)[2:23689,seq(1, ncol(eset), 4)]) # These columns contain normalized Red intensity in each data file. red = do.call(cbind, red1) green1 = lapply(fullset1,function(eset) exprs(eset)[2:23689,seq(2, ncol(eset), 4)]) # These columns contain normalized Green intensity in each data file. green = do.call(cbind, green1) 2) Normalizing between arrays: I am using normalizeBetweenArrays (method=quantile) for merged data set so that the intensities have similar distributions across the series of arrays. So I did following: rgl1 = new("RGList", list(R=red, G=green)) norm1 = normalizeBetweenArrays(rgl1, method="quantile") And got error: Error in log(R, 2) : Non-numeric argument to mathematical function. Why this error?? Then I tried to normalize red and green intensities separately by doing this normR1 = normalizeBetweenArrays(red, method="quantile") normG1 = normalizeBetweenArrays(green, method="quantile") and it worked! Why?? 3) Quality assessment of the merged data set: For quality assessment I am using arrayQualityMetrics package. To check if quality assessment on separately normalized red and green intensities can be performed I did following: rgl1 = new("RGList", list(R=normRed1, G=normGreen1)) qmrgl1 = arrayQualityMetrics(rgl1, "QMrgl1") # Here the package is accepting expression data as RGList (rgl1) and will generate HTML report and save in QMrgl1 folder. But with no luck I got error: Error in rc - gc : non-numeric argument to binary operator I am really stuck and running out of idea. Please help me to rectify these errors. Thanks in advance. Best! Amit

Hi Amit, from your error: > Error in log(R, 2) : Non-numeric argument to > mathematical function. this means that the code is trying to log transform non-numerical data, which usually means at least one of your numbers is actually a character, thus the whole column becomes characters. I'd check your "R" object thoroughly for the presence of "character" data Mark On 30/09/2009, at 6:33 AM, Amit Kumar wrote: > Dear All, > > I am working with 13 different data sets (containing 550 arrays in > total) which is normalized using general linear model for print-tip. I > am trying to do following: > > 1) Merging all 13 different data sets: > To merge these data sets I built ExpressionSet for each data set. Then > I made a list of these ExpressionSets and named it "fullset1". Then to > merge red and green intensity I did following: > > red1 = lapply(fullset1,function(eset) exprs(eset)[2:23689,seq(1, > ncol(eset), 4)]) # These columns contain normalized Red intensity in > each data file. > red = do.call(cbind, red1) > > green1 = lapply(fullset1,function(eset) exprs(eset)[2:23689,seq(2, > ncol(eset), 4)]) # These columns contain normalized Green intensity in > each data file. > green = do.call(cbind, green1) > > 2) Normalizing between arrays: > I am using normalizeBetweenArrays (method=quantile) for merged data > set so that the intensities have similar distributions across the > series of arrays. So I did following: > > rgl1 = new("RGList", list(R=red, G=green)) > norm1 = normalizeBetweenArrays(rgl1, method="quantile") > > And got error: Error in log(R, 2) : Non-numeric argument to > mathematical function. Why this error?? > > Then I tried to normalize red and green intensities separately by > doing this > normR1 = normalizeBetweenArrays(red, method="quantile") > normG1 = normalizeBetweenArrays(green, method="quantile") > and it worked! Why?? > > 3) Quality assessment of the merged data set: > For quality assessment I am using arrayQualityMetrics package. To > check if quality assessment on separately normalized red and green > intensities can be performed I did following: > rgl1 = new("RGList", list(R=normRed1, G=normGreen1)) > qmrgl1 = arrayQualityMetrics(rgl1, "QMrgl1") # Here the package is > accepting expression data as RGList (rgl1) and will generate HTML > report and save in QMrgl1 folder. > > But with no luck I got error: Error in rc - gc : non-numeric argument > to binary operator > > I am really stuck and running out of idea. Please help me to rectify > these errors. Thanks in advance. > > Best! > Amit > > _______________________________________________ > 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