One directional spatial normalisation for microarray data
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@michael-watson-iah-c-378
Last seen 8.4 years ago
Hi I'm looking for a normalisation procedure which will normalise log ratio based on row only. I know the marray package has 2D normalisation, but I fired that at my data and it didn't touch it - the data I have is independent of column, but very dependent on row. Is there anything? Thanks Mick The information contained in this message may be confide...{{dropped:14}}
marray marray • 366 views
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@henrik-bengtsson-4333
Last seen 5 weeks ago
United States
Hi, just to make sure - the systematic effects you have, is it possible that they are due to variability between microtiter plates? Since you say you only have spatial effects in one direction, this could the case. If so, when spotting arrays from such plates row by row (or column by column), in an NxN grid of print tips, each print-tip group/grid will show horizontal (or vertical) bands. See H. Bengtsson, Identification and normalization of plate effect in cDNA microarray data, Preprints in Mathematical Sciences, 2002:28, Mathematical Statistics, Lund University, 2002. URL: http://www.maths.lth.se/bioinformatics/publications/ Do you have bands like in left panel of Figure 1. If you plot the data in print order, you might then get what is in Figure 2. If so, it is very likely there is print-order (print-dip) effect in you data. *HOWEVER*, this does *not* mean that you should do print-order normalization (early on I did said you should do this, but I know better know). Instead, think about it this way. If different plates gives different probe *intensities*, and this is expected, an intensity-dependent artifact in log-ratios will the show up as a printorder effect ("symptom") on log-ratios. However, if you remove intensity-dependent artifacts in you log-ratios, the printorder symptoms should go away. If it doesn't, you can probably to a better job in removing intensity-dependent artifacts. I don't have final documentation on this, but I think the following talk will illustrate it all: H. Bengtsson, Plate Effects in cDNA Microarray Data, Statistics Department, University of California in Berkeley. September 26, 2002. URL: http://www.maths.lth.se/bioinformatics/calendar/20020926/ In the aroma package (http://www.braju.com/R/) there are several different plot functions that allows you to plot your data in printtip/-dip order. Hope this helps Henrik On 26/11/2007, michael watson (IAH-C) <michael.watson at="" bbsrc.ac.uk=""> wrote: > Hi > > I'm looking for a normalisation procedure which will normalise log ratio > based on row only. I know the marray package has 2D normalisation, but > I fired that at my data and it didn't touch it - the data I have is > independent of column, but very dependent on row. > > Is there anything? > > Thanks > Mick > > The information contained in this message may be confide...{{dropped:14}} > > _______________________________________________ > 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 >
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