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Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset

Sung E Choe1,2, Michael Boutros1,6, Alan M Michelson1,2,3, George M Church1 and Marc S Halfon2,4,5*

1 Department of Genetics, Harvard Medical School, New Research Building, 77 Avenue Louis Pasteur, Boston, MA 02115, USA

2 Division of Genetics, Department of Medicine, Brigham and Women's Hospital, New Research Building, 77 Avenue Louis Pasteur, Boston, MA 02115, USA

3 Howard Hughes Medical Institute, Brigham and Women's Hospital, 20 Shattuck Street, Boston, MA 02115, USA

4 Department of Biochemistry, 140 Farber Hall, 3435 Main St., SUNY at Buffalo, Buffalo, NY 14214, USA

5 Center of Excellence in Bioinformatics, 140 Farber Hall, 3435 Main St., SUNY at Buffalo, Buffalo, NY 14214, USA

6 German Cancer Research Center (DKFZ/B110), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany

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Genome Biology 2005, 6:R16 doi:10.1186/gb-2005-6-2-r16

Published: 28 January 2005

Additional files

Additional data file 1:

A figure and explanatory legend showing the degree of overlap between two lists of differentially expressed genes

Format: DOC Size: 41KB Download file

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Additional data file 2:

All analysis option combinations used to generate the expression summary datasets in this study

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Additional data file 3:

A plot of observed vs actual spiked-in fold changes at the probe level

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Additional data file 4:

An example of asymmetric M (log2 fold change) vs A (average log2 signal) plot for the comparison of two biological samples

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Additional data file 5:

A comparison of the analysis methods with respect to the detection of DEGs with low signal

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Additional data file 6:

A Zip archive containing plain text files (in Affymetrix CEL format), Affymetrix *.CEL files for the C chips in this dataset

Format: ZIP Size: 8.7MB Download file

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Additional data file 7:

A Zip archive containing plain text files (in Affymetrix CEL format), Affymetrix *.CEL files for the S chips in this dataset

Format: ZIP Size: 8.9MB Download file

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Additional data file 8:

Detailed information for the individual DGC clones used in this study

Format: XLS Size: 853KB Download file

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