Entering edit mode
Dear John,
You do need to normalize between arrays if you want to do a single
channel analysis. It is true that normalization is more difficult if
there are very large differences between samples, but you have to do
the best you can. I personally use Aquantile in most cases, based on
unpublished studies in my own group.
Best wishes
Gordon
>Date: Sun, 22 Apr 2007 03:07:55 +0000 (UTC)
>From: John Fowler <fowlerj at="" science.oregonstate.edu="">
>Subject: [BioC] Suitability of normalizeBetweenArrays? - arrays with
> very different characteristics
>To: bioconductor at stat.math.ethz.ch
>
>Hello all,
>
>I am looking for advice on whether it is suitable to use
>normalizeBetweenArrays
>(in limma) in my two-color array experiment. Secondarily, if it is
NOT
>appropriate, would that also preclude doing a single channel analysis
of my
>data? It seems that the User's Guide indicates that some form of
normalizing
>between arrays is recommended before doing the single channel
analysis.
>
>I have a 3x2 loop design, with three different developmental stages &
two
>different genotypes, four replicates each. I am using spotted long
oligo
>arrays, two colors. Because the two genotypes have very few
expression
>differences between them, but two of the developmental stages appear
>to be VERY
>different, the results on my arrays are also different. On arrays
>in which the
>same developmental stage, but different genotypes, are used, the data
are
>primarily clustered around M=0, distributed along the A axis. And,
>as you would
>expect, when the very different developmental stages of the same
genotype are
>used, the amount of variation in M (and presumably in A, as well,
although
>that's more difficult to see) is obvious in the plots.
>
>So, is it in-advisable to use normalizeBetweenArrays in this case?
My best
>guess as to the most appropriate method to use would be "Aquantile",
but I am
>unsure of that, as well.
>
>I would be happy for suggestions on these questions -
>
>thank you very much,
>John
>
>John Fowler
>Associate Professor
>Oregon State University
