Changes on AFGC website for helping with analyzing microarray data

Lorne Rose larose at Andrew2.Stanford.EDU
Wed Jan 31 13:44:22 EST 2001

Hi all,

Several guides have been added to the AFGC website
( under the Microarray heading. If you are
planning on looking at any of the AFGC data in the Stanford
Microarray Database (SMD), please look at these guides.

The first of these guides is "Analyzing AFGC Microarray Data". In it
you will find helpful tips on how to examine AFGC microarray data.

The second guide to be added is a "Guide to Flagging spots". With
changes in analysis programs and within the Stanford Microarray
Database, the way flag filters need to be set have changed for
AFGC experiments. This guide goes over how technicians flagged
spots based on whether it was bad or saturated, and what values
the different flags will have in SMD.

The final two guides that have been recently added, explain
changes made to Cycle 1 experiments that were either reanalyed
or redone. In "The Switch from Scanalyze to Genepix," you will find
information on why the AFGC experiments are now being analyzed
using Genepix Pro 3.0, and which experiments during cycle 1were
reanalyzed and made public using this new software. Te "Redone
Experiment Information" guide, explains some of the quality control
problems faced while doing the Cycle 1 experiments, and which
experiments were redone due to these problems.

If you plan on analyzing any AFGC Microarray data, it is important
that each of these guides be veiwed before starting you analysis.


Lorne Rose
Carnegie Institution
Research Technician
(650)325-1521 ext.242
larose at


More information about the Arab-gen mailing list