From n.haigh at sheffield.ac.uk  Mon Aug  6 07:33:06 2007
From: n.haigh at sheffield.ac.uk (Nathan Haigh)
Date: Mon, 06 Aug 2007 12:33:06 +0100
Subject: [Bio-Linux] Bioconductor - save as CEL file
Message-ID: <46B706F2.1000206@sheffield.ac.uk>

I have a need to create a CEL file containing the median raw intensity
values from 4 replicate arrays. Does anyone know if/how this can be done
using bioconductor?

Further details:
I'm using the xspecies approach [1] to mask out low intensity probes
from a gDNA hybridisation of a close relative of A. thaliana to the ATH1
affy chip. The script that is provided for doing the masking out of
probes, only works on a single CEL file. However, I have 4 reps and
would like to make use of them, so thought it best to generate a pseudo
CEL file from the medians of those 4 reps, but don't know if this is
possible. I will apply some normalisation steps to the 4 reps to ensure
they are comparable and that taking a median across the reps is OK.

If anyone can help with how to save these data to a CEL file, i'd be
really appreciative.

Cheers
Nath


Refs:
[1] - http://affymetrix.arabidopsis.info/xspecies/