> Message: 1 > Date: Fri, 30 Jan 2004 09:02:04 -0600 > From: Joyce Gu <jwgu@bcm.tmc.edu> > Subject: [BioC] Normalization with cDNA array > Hello, > There are two ways to normalize the data, one is location normalization, the > other is scale normalization in marrayClasses. I am wondering what kind of > situation should we use location normalization,and when should we use scale > normalization? > Does anyone has any suggession? The choice of normalisation method usually depends upon the quality of the data. With cDNA arrays you generally want to remove dye bias effects along with any spatial effects, so print-tip loess normalisation is generally advised (method=PrintTipLoess in maNorm). If some of the print-tip groups still have a large spread compared to other print-tip groups on the array (look at the box plots of M values) you can use scale normalisation to correct for this (assuming the effect isn't due to a large number of DE genes in those print-tip groups). For a description of different normalisation methods have a look at http://www.statsci.org/smyth/pubs/normalize.pdf Smyth, G. K., and Speed, T. P. (2003). Normalization of cDNA microarray data. In: METHODS: Selecting Candidate Genes from DNA Array Screens: Application to Neuroscience, D. Carter (ed.). Methods Volume 31, Issue 4, December 2003, pages 265-273. and Yang, Y. H., Dudoit, S., Luu, P., Lin, D. M., Peng, V., Ngai, J., and Speed, T. P. (2002). Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Research 30(4):e15. Cheers Chris -- Dr Chris Wilkinson Research Officer (Bioinformatics) | Visiting Research Fellow Child Health Research Institute (CHRI) | Microarray Analysis Group 7th floor, Clarence Rieger Building | Room 121 Women's and Children's Hospital | School of Applied Mathematics 72 King William Rd, North Adelaide, 5006 | The University of Adelaide, 5005 Math's Office (Room 121) Ph: 8303 3714 CHRI Office (2nd floor) Ph: 8161 6363 Christopher.Wilkinson@adelaide.edu.au http://mag.maths.adelaide.edu.au/crwilkinson.html