Hello, You can check this by calculating the mean intensity per chip which should be 150. regards, Arne > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch]On Behalf Of Xiao Shi > Sent: Friday, August 26, 2005 9:01 > To: bioconductor at stat.math.ethz.ch > Subject: [BioC] Do i need to do scaling normalization to the data i > downloadform NCBI GEO? > > > Hi everybody, > Sorry,maybe this is not a bioconductor question,but someone > in this list may > know the answer.I want to re-analysis a microarray data set in GEO( > http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1159) > .The data i > download are Intensities value from MAS5.0 as indicated on NCBI > GEO.Thecorresponding article > (Prognostically useful gene-expression profiles in acute > myeloid leukemia,PMID: > 15084694) described the Normalization procedures as follow: > > 1. All intensity values were scaled to an average value of 150 per > GeneChip according to the method of global scaling, or > normalization, provided > in the Affymetrix Microarray Suite software, version 5.0 (MAS5.0). > 2. Since their methods reliably identify samples with an average > intensity value of 30 or more but do not reliably > discriminate values > between 0 and 30, these values were set to 30. > 3. Analysis > > My question,Do i need to do scaling normalization (to 150 per > GeneChip) to > the data i download form NCBI GEO? > Thanks in advance. > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >