Sir When I use the following script celfiles <- read.affy(covdesc="phenodataa.txt", path="dataa") I get the following error message: Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line 1 did not have 4 elements phenodataa.txt has 50 rows and 3 columns I looked at line 1 and it has all 3 columns. phenodataa.txt file looks like this Name FileName Target GSM317649.CEL dataa/GSM317649.CEL control GSM317650.CEL dataa/GSM317650.CEL depression GSM317651.CEL dataa/GSM317651.CEL depression GSM317653.CEL dataa/GSM317653.CEL bipolar disorder GSM317654.CEL dataa/GSM317654.CEL schizophrenia GSM317655.CEL dataa/GSM317655.CEL schizophrenia GSM317656.CEL dataa/GSM317656.CEL bipolar disorder GSM317657.CEL dataa/GSM317657.CEL depression GSM317658.CEL dataa/GSM317658.CEL bipolar disorder GSM317659.CEL dataa/GSM317659.CEL schizophrenia GSM317660.CEL dataa/GSM317660.CEL bipolar disorder GSM317661.CEL dataa/GSM317661.CEL schizophrenia GSM317662.CEL dataa/GSM317662.CEL schizophrenia GSM317663.CEL dataa/GSM317663.CEL bipolar disorder GSM317664.CEL dataa/GSM317664.CEL bipolar disorder GSM317665.CEL dataa/GSM317665.CEL bipolar disorder GSM317666.CEL dataa/GSM317666.CEL control GSM317667.CEL dataa/GSM317667.CEL depression GSM317668.CEL dataa/GSM317668.CEL schizophrenia GSM317669.CEL dataa/GSM317669.CEL schizophrenia GSM317670.CEL dataa/GSM317670.CEL depression GSM317671.CEL dataa/GSM317671.CEL schizophrenia GSM317672.CEL dataa/GSM317672.CEL control GSM317673.CEL dataa/GSM317673.CEL bipolar disorder GSM317674.CEL dataa/GSM317674.CEL depression GSM317675.CEL dataa/GSM317675.CEL depression GSM317676.CEL dataa/GSM317676.CEL schizophrenia GSM317677.CEL dataa/GSM317677.CEL depression GSM317678.CEL dataa/GSM317678.CEL depression GSM317679.CEL dataa/GSM317679.CEL control GSM317680.CEL dataa/GSM317680.CEL schizophrenia GSM317681.CEL dataa/GSM317681.CEL control GSM317682.CEL dataa/GSM317682.CEL control GSM317683.CEL dataa/GSM317683.CEL control GSM317684.CEL dataa/GSM317684.CEL schizophrenia GSM317685.CEL dataa/GSM317685.CEL schizophrenia GSM317686.CEL dataa/GSM317686.CEL bipolar disorder GSM317687.CEL dataa/GSM317687.CEL depression GSM317688.CEL dataa/GSM317688.CEL bipolar disorder GSM317689.CEL dataa/GSM317689.CEL control GSM317690.CEL dataa/GSM317690.CEL bipolar disorder GSM317691.CEL dataa/GSM317691.CEL control GSM317692.CEL dataa/GSM317692.CEL control GSM317693.CEL dataa/GSM317693.CEL control GSM317694.CEL dataa/GSM317694.CEL schizophrenia GSM317695.CEL dataa/GSM317695.CEL depression GSM317696.CEL dataa/GSM317696.CEL control GSM317697.CEL dataa/GSM317697.CEL control GSM317698.CEL dataa/GSM317698.CEL control I checked whether there is any empty space or tabs..can't find anything. Can't able to sort out the error. -- *Laya Rose* [[alternative HTML version deleted]]

Your metadata file is in the wrong format. The first column should not have any heading.