I was using "separate channel analysis of two-color data" for data from 17 Agilent 44K oligomer arrays and had error massages for wihich I copied and pasted below: > targets2.sc channel.col FileNames Target 1.1 1 29N.txt ant.con 1.2 2 29N.txt lat.con 2.1 1 273N.txt lat.con 2.2 2 273N.txt ant.con 3.1 1 283N.txt lat.con 3.2 2 283N.txt ant.con 4.1 1 267N.txt ant.con 4.2 2 267N.txt lat.con 5.1 1 281N.txt lat.con 5.2 2 281N.txt ant.con 6.1 1 289N.txt lat.con 6.2 2 289N.txt ant.con 7.1 1 103R.txt ant.res 7.2 2 103R.txt lat.res 8.1 1 105R.txt lat.res 8.2 2 105R.txt ant.res 9.1 1 104R.txt ant.res 9.2 2 104R.txt lat.res 10.1 1 213R.txt lat.res 10.2 2 213R.txt ant.res 11.1 1 338R.txt lat.res 11.2 2 338R.txt ant.res 12.1 1 2D.txt ant.dys 12.2 2 2D.txt lat.dys 13.1 1 101D.txt lat.dys 13.2 2 101D.txt ant.dys 14.1 1 425D.txt lat.dys 14.2 2 425D.txt ant.dys 15.1 1 53D.txt ant.dys 15.2 2 53D.txt lat.dys 16.1 1 424D.txt lat.dys 16.2 2 424D.txt ant.dys 17.1 1 53D_2.txt lat.dys 17.2 2 53D_2.txt ant.dys > u <- uniquetargets2.sc$Target) > f <- factortargets2.sc$target, levels=u) > design <- model.matrix(~0+f) Warning message: is.na() applied to non-(list or vector) in: is.na(rows) > colnames(design) <- u > dim(design) [1] 0 6 > dim(f) NULL > corfit <- intraSpotCorrelation(MA2, design) Error: couldn't find function "intraSpotCorrelation" > fit <- lmscFit(MA2, design, correlation=corfit$consensus) Error in lmscFit(MA2, design, correlation = corfit$consensus) : The number of rows of the design matrix should match the number of channel intensities, i.e., twice the number of arrays > ?intraSopt> corfit <- intraspotCorrelation(MA2, design) Error in intraspotCorrelation(MA2, design) : The number of rows of the design matrix should match the number of channel intensities, i.e., twice the number of arrays ******************************** It seems the codes for design file is wrong. I looked model.matrix but didn't get clues. Can you help me out? Thanks. Wayne