Dear all, On my microarray I have some genes for which I have duplicate probes, but not for all. Before I do the stats I would like to average the duplicate probes (e.g. GB10001-RA and GB10006-RA in the example below). So I have a limma RGList object, with the gene names stored in RG$genes$GeneName and I would like to average the R / G expression values (on a Log scale) for all probes for which I have replicate spots (ideally it should work for any number of replicate spots, no replicate, or 1, 2 or more replicates). Does anybody have any ideas what would be the most elegant way to average out expression values based on the occurrence of duplicate entries in RG$genes$GeneName? Limma can only average duplicates if you have the same nr of replicates per probe, so that doesn't work for me... For the same reason I also can't use the DuplicateCorrelation() function... cheers, Tom > RG[1:5,] An object of class "RGList" $R sample1 sample2 sample3 sample4 ... sample16 [1,] 26.78257 29.0004 25.0079 26.39580 [2,] 43.38434 28.8024 26.6724 25.95790 [3,] 10714.26000 9939.5930 8176.1090 7799.02200 [4,] 104.95700 111.3113 106.5972 82.49293 [5,] 8381.44300 7420.4830 7276.8480 8260.76500 $G sample1 sample2 sample3 sample4 .... sample16 [1,] 23.70600 27.56034 26.02305 28.05054 [2,] 43.21391 27.92983 27.30349 27.08347 [3,] 7163.33400 7767.61200 9167.84500 10383.52000 [4,] 53.17878 73.86636 129.05350 92.27209 [5,] 5974.27400 8053.11300 7722.92500 7193.23000 $targets [1] "sample1.txt" "sample2.txt" "sample3.txt" "sample4.txt" ... "sample16.txt" $genes FeatureNum Row Col ProbeName ControlType GeneName Description SystematicName Status 10005 10015 123 11 MAF_Amel_000001 0 GB10001-RA Unknown GB10001-RA gene 11060 11071 136 1 MAF_Amel_000002 0 GB10001-RA Unknown GB10001-RA gene 7355 7363 90 65 MAF_Amel_000003 0 GB10006-RA Unknown GB10006-RA gene 1433 1435 18 41 MAF_Amel_000004 0 GB10006-RA Unknown GB10006-RA gene 13775 13789 169 13 MAF_Amel_000005 0 GB10007-RA Unknown GB10007-RA gene $source [1] "agilent"