Hi I wasn't sure if I was emailing the appropriate person but If you could point me in the right direction that would be much appreciated. Recently my group obtained R and the Bioconductor packages for Normalisation and analysis of cDNA microarray data. (marrayNorm etc.) having looked at most of the documentation I was wondering if it is possible to exclude background information from marrayInput and/or subsequent normalisation procedures, if so what the options would be ? read.marrayRaw currently needs name.Gb & name.Rb ???? which is data we would like to exclude on occasions Apologies I'm a Biologist and new to this Bioinformatics stuff Best regards Jason ************************************* Jason Skelton Drosophila Functional Genomics Department of Genetics Cambridge University CB2 3EH UK 01223 765927 www.gen.cam.ac.uk/~flychip/ ***************************************

Hi Jason, > having looked at most of the documentation I was wondering if it is > possible to exclude background information from marrayInput and/or > subsequent normalisation procedures, > if so what the options would be ? > read.marrayRaw currently needs name.Gb & name.Rb ???? which is data we > would like to exclude on occasions Yes, that is possible. There is two ways of doing it. 1) Either use read.marrayRaw and don't put any argument for name.Gb and name.Rb e.g. read.marrayRaw("test.gpr", name.Gf="F532 Mean", name.Rf="F635 Mean") 2) If you are using data from GenePix or Spot you can use the function read.GenePix and read.Spot which has a few defaults argument. In those cases you can set the background to zero at a later stage: e.g. y <- read.GenePix("test.gpr") maGb(test) <- matrix(0,0,0) maRb(test) <- matrix(0,0,0) The rest of the normalization and anlaysis plot will then be perform with no background subtraction. Cheers Jean