[BioC] Help:How to do normalization with Ambion bioarray data?

[Al Ivens]

Hi,

A suggestion might be to have a look at the replicate spacing; from the
only Ambion arrays I have tried to analyse, they "helpfully" have the
control blocks as "top left" and "bottom right" on each slide, so the
top array layout is NOT the same as the bottom array layout within each
gpr.

So, when you define spacing = x within limma, none of the duplicates
actually "line up" with each other, assuming you are wanting to treat
the two duplicates on each slide in this way.  I got around it by
reordering the second half of gpr file to give a constant spacing, then
proceeding as usual with limma.

HTH,

al


> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch 
> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of 
> julin at aecom.yu.edu
> Sent: 07 December 2006 18:30
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] Help:How to do normalization with Ambion 
> bioarray data?
> 
> 
> Dear All:
> 
> Recently I did some Ambion bioarray (one color 
> hybridization), and got data of 6 arrays in 3 gpr files(in 
> each gpr file there will be two array which being designated 
> as block1 and block 2)from GenePix. I am having trouble to 
> normalize my data. Can anyone kindly give me any clue? Thanks a lot!
> 
> Qingping Cui
> Albert Einstein Cancer Center
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch 
> https://stat.ethz.ch/mailman/listinfo/biocondu> ctor
> Search the 
> archives: 
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>