No longer operational

Spatial Flaw Detection for Affymetrix GeneChips

HG-U133 2+ only so far. Process CEL file (will take at least a minute).

Normalisation and error detection at probe level described in:
W. B. Langdon and G. J. G. Upton and R. da Silva Camargo and A. P. Harrison, A Survey of Spatial Defects in Homo Sapiens Affymetrix GeneChips, IEEE/ACM Transactions on Computational Biology and Bioinformatics, accepted.
PDF gzip ps R code example

Example

affy image of a compressed HG_U133 2+ CEL file from the Gene Expression Omnibus GEO

Red indicates suspiciously large areas which either are below average or above average after row quantile normalisation.

A total of 4977 probes are suspect, more than forty times the number that would be expected by random chance.

Example GSM253203.CEL CEL file and corresponding output

CAMDA-2007 slides

Quantile Normalisation of a single Affymetrix GeneChip CEL file

HG-U133 2+ only so far.
Normalizing each CEL file will take at least 26 minutes (will timeout after 1.5 hours).
(Binary CEL files are not yet supported. Use CellFileConversionTool.exe and CellIO70.dll from Affymetrix.com to convert binary to text?)

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