Genome Biology
Volume 6
Issue 2

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Research

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

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

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

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

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

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

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

author email corresponding author email

Genome Biology 2005, 6:R16doi:10.1186/gb-2005-6-2-r16


Published:	28 January 2005

Subject areas: Genome studies, Methods

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 (log₂fold change) vs A (average log₂signal) 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: 9MB Download file

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