Dear colleagues, I loaded data from some cDNA arrays into limma and maanova/R separately and was checking if my arrays were ok. I ran imageplot in limma and arrayview in maanova, and to my surprise the images looked very different. I have put the images of the first six arrays on http://www-gene.cimr.cam.ac.uk/todd/arrayview/ image-M-1-6.png is the limma output, the others png files came from maanova. Are they not plotting the same thing (log ratio)? I didn't get any background values so I plotted M. Arrayview005.png shows a streak which is not visible in QPG185 (same array) in limma. And I don't understand why there are regular blocks of almost solid red or green in the limma output. I didn't remove landlites and controls (but gave them 0 weight in limma) but they are supposed to be regularly spaced. And the images from maanova differ a lot in how red or green they are. Should I worry about the quality of these arrays? Limma code: MA<-normalizeWithinArrays(RG) imageplot3by2(MA, z="M") Maanova code: data.raw<-read.madata(...) arrayview(data.raw, array=1:6) Any help would be greatly appreciated. Many thanks, Alex ------------------------------------ Alex Lam PhD student Department of Genetics and Genomics Roslin Institute (Edinburgh) Roslin Midlothian EH25 9PS Phone +44 131 5274471 Web http://www.roslin.ac.uk

Dear Dr. Smyth, I figured out what went wrong with my previous imageplot. In my data files and gal file the rows were sorted by gene names. I re-sorted the rows by spot number and reloaded the files. Now the images are now much more even, and the streak noticed on the 5th array on the maanova spatial plot is now visible. http://www-gene.cimr.cam.ac.uk/todd/arrayview/new-image-M-1-6.png Thanks, Alex ------------------------------------ Alex Lam PhD student Department of Genetics and Genomics Roslin Institute (Edinburgh) Roslin Midlothian EH25 9PS Phone +44 131 5274471 Web http://www.roslin.ac.uk -----Original Message----- From: alex lam (RI) Sent: 06 February 2006 17:44 To: 'bioconductor at stat.math.ethz.ch' Cc: 'smyth at wehi.edu.au'; 'gary.churchill at jax.org' Subject: diagnostics Dear colleagues, I loaded data from some cDNA arrays into limma and maanova/R separately and was checking if my arrays were ok. I ran imageplot in limma and arrayview in maanova, and to my surprise the images looked very different. I have put the images of the first six arrays on http://www-gene.cimr.cam.ac.uk/todd/arrayview/ image-M-1-6.png is the limma output, the others png files came from maanova. Are they not plotting the same thing (log ratio)? I didn't get any background values so I plotted M. Arrayview005.png shows a streak which is not visible in QPG185 (same array) in limma. And I don't understand why there are regular blocks of almost solid red or green in the limma output. I didn't remove landlites and controls (but gave them 0 weight in limma) but they are supposed to be regularly spaced. And the images from maanova differ a lot in how red or green they are. Should I worry about the quality of these arrays? Limma code: MA<-normalizeWithinArrays(RG) imageplot3by2(MA, z="M") Maanova code: data.raw<-read.madata(...) arrayview(data.raw, array=1:6) Any help would be greatly appreciated. Many thanks, Alex ------------------------------------ Alex Lam PhD student Department of Genetics and Genomics Roslin Institute (Edinburgh) Roslin Midlothian EH25 9PS Phone +44 131 5274471 Web http://www.roslin.ac.uk