[BioC] diagnostics

[alex lam (RI)]

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