Improved precision and accuracy for microarrays using updated probe set definitions

doi:10.1186/1471-2105-8-48

BMC Bioinformatics

Volume 8

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Correspondence

Improved precision and accuracy for microarrays using updated probe set definitions

Rickard Sandberg¹ and Ola Larsson²

¹Massachusetts Institute of Technology, Department of biology, 68-211, Cambridge, MA 02139, USA

²University of Minnesota, Department of Medicine, MMC 276, Minneapolis, MN 55455, USA

author email corresponding author email

BMC Bioinformatics 2007, 8:48doi:10.1186/1471-2105-8-48


Published:	8 February 2007

Additional files

Additional file 1:

Precision for the data from each laboratory. Similarly to main figure 1, we compared the precision in microarray experiments when using the updated probe set definitions in comparison with the original one for each lab independently. We measured the precision as the Pearson correlation between the log2 ratios of expression levels obtained using GCRMA. The x-axis show the number of probes integrated into each probe set. We grouped the number of probes into intervals of four in order to obtain a sufficiently large number of probe sets to get a robust estimate of each data point. The grouping is identical to Figure 1a.

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Additional file 2:

RT-PCR Map. A table (cvs file) with the identifiers used to associate the RT-PCR data from ref. 11 to the expression estimates derived using different updated probe set definitions.

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Additional file 3:

Accuracy for GCRMA data. Table with accuracy estimates for the different updated probe set definitions using GCRMA data. All tests were performed as described for Table 3.

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