> >I just wonder is there any option to do normalization in limmaGUI or limma > >WITHOUT background subtraction? > > RG <- backgroundCorrect(RG,method="none") > MA <- normalizeWithinArrays(RG) > > Note: you need a more recent version of limma than the BioC release 1.2. > > Gordon Avoiding background subtraction in this way is not yet possible in limmaGUI via widgets, but you can always edit copies of your image analysis files (Spot or GenePix or ...) to include columns of zeroes for the background. Soon I will be adding some documentation to limmaGUI, to make it easier to fiddle with the internal limma objects via the "Evaluate R Code" window. You can do RG <- backgroundCorrect(RG,method="none") But then any existing MA objects will be out of date, so it's best to start a new analysis, then run the backgroundCorrect command above, then check the value of MA.Available via the Evaluate R Code window will show you that the only MA object which has been automatically created is MAraw (unnormalized), (not MAwithinArrays, MAbetweenArrays or MAboth), so you should overwrite this with MAraw <- MA.RG(RG) after using background correct "none" to overwrite the default RG. Unless you've been doing some serious "hacking" :) the values in the MA.Available list object seen in the "Evaluate R Code" window should be consistent with those in the drill-down status widget. Regards, James ---------------------------------------------------------------------- ---- James Wettenhall Tel: (+61 3) 9345 2629 Division of Genetics and Bioinformatics Fax: (+61 3) 9347 0852 The Walter & Eliza Hall Institute E-mail: wettenhall@wehi.edu.au of Medical Research, Mobile: (+61 / 0 ) 438 527 921 1G Royal Parade, Parkville, Vic 3050, Australia http://www.wehi.edu.au