17%20SAM%20Test%203_27_08

17%20SAM%20Test%203_27_08 - Significance Analysis of...

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1 1 Significance Analysis of Microarrays (SAM) Peng Liu 3/27/2008 2 Significance Analysis of Microarrays (SAM) ± Tusher, V. G., Tibshirani, R., and Chu, G. (2001). Significance analysis of microarrays applied to the ionizing radiation response. Proceedings of the National Academy of Sciences 98(9) , 5116-5121. ± See http://www-stat.stanford.edu/~tibs/SAM/ for more recent developments. 3 Motivating Experiment Human Cell Lines Treatment Irradiated (I) Unirradiated (U) 1 One RNA sample for each combination of cell line and treatment 2 4 Motivating Experiment Treatment Irradiated (I) Unirradiated (U) 1 U1A U1B U2A U2B I1A I1B I2A I2B After labeling, each RNA sample was split into two aliquots denoted A and B. 2
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2 5 Motivating Experiment Human Cell Lines Treatment Irradiated (I) Unirradiated (U) 1 U1A U1B U2A U2B I1A I1B I2A I2B 8 GeneChips, one for each sample, were used to obtain measures of expression. 2 6 The Measure of Expression ± The Tusher et al. paper appeared before much work had been done on computing expression measures from PM and MM intensities. ± It appears that they used something similar to an average of PM-MM intensities over the probe pairs in a probe set as their expression measure. ± They conducted a regression-based normalization in which each GeneChip was normalized to the average over all GeneChips. ± Furthermore they worked with normalized data on the original rather than the log scale.
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17%20SAM%20Test%203_27_08 - Significance Analysis of...

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