I have a question regarding the effect of different scanners on cDNA slides. I have data for a small (8 slide) microarray experiment. These slides were hybridised and scanned at another facility, and for reasons that are not quite clear to me, were scanned again once our local facility was up and running. Based on the MA plots, it appears the gain was turned up on the second set of scans wrt the first. The first scan has a distinct red dye bias at low intensity, whilst the second scan has a smaller green dye bias, and larger intensities (avg intensities start at 2^7 vs 2^6 and max intensities are higher). With regard to the analysis, I'm not sure how to rate one set of scans over the other. I've analysed each seperately, and also combined them treating the different scans as technical replicates. I figure that the different scans are highly correlated technical replicates - very similar to the case of using adjacent duplicate spots. To test this out I created an MA object from getting normalised MA objects from the two scans and then combining them so I had an array with twice the normal number of spots and with adjacent spots representing the same cDNA, but different scans. This allowed me to use the dupcor.series function of limma to estimate the spatial correlation (about 0.32 with IQR from of (0,0.6)) to use in gls.series. However given that background is different between the slides I'm not sure if this approach is really that valid. I've also looked at the overlap of the top50 genes (ranked on interaction parameter) from each analysis scan 1 vs 2 = 28 scan 1 vs combined = 28 scan 2 vs combined = 42 scan 1 vs scan2 vs combined = 44 Essentially I'm interested in opinions on how to handle the problem of which scan to use. I can arbitrarily (or randomly) use one of the scans, but I was wondering if anything can be gained from the use of two physically different scanners (or have I just picked up another source of variation)... 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 (CR2 52A) Ph: 8161 6363 Christopher.Wilkinson@adelaide.edu.au http://mag.maths.adelaide.edu.au/crwilkinson.html