Relative power and sample size analysis on gene expression profiling data. Export

@article{citeulike:5801492, abstract = {BACKGROUND: With the increasing number of expression profiling technologies, researchers today are confronted with choosing the technology that has sufficient power with minimal sample size, in order to reduce cost and time. These depend on data variability, partly determined by sample type, preparation and processing. Objective measures that help experimental design, given own pilot data, are thus fundamental. RESULTS: Relative power and sample size analysis were performed on two distinct data sets. The first set consisted of Affymetrix array data derived from a nutrigenomics experiment in which weak, intermediate and strong PPARalpha agonists were administered to wild-type and PPARalpha-null mice. Our analysis confirms the hierarchy of PPARalpha-activating compounds previously reported and the general idea that larger effect sizes positively contribute to the average power of the experiment. A simulation experiment was performed that mimicked the effect sizes seen in the first data set. The relative power was predicted but the estimates were slightly conservative. The second, more challenging, data set describes a microarray platform comparison study using hippocampal deltaC-doublecortin-like kinase transgenic mice that were compared to wild-type mice, which was combined with results from Solexa/Illumina deep sequencing runs. As expected, the choice of technology greatly influences the performance of the experiment. Solexa/Illumina deep sequencing has the highest overall power followed by the microarray platforms Agilent and Affymetrix. Interestingly, Solexa/Illumina deep sequencing displays comparable power across all intensity ranges, in contrast with microarray platforms that have decreased power in the low intensity range due to background noise. This means that deep sequencing technology is especially more powerful in detecting differences in the low intensity range, compared to microarray platforms. CONCLUSION: Power and sample size analysis based on pilot data give valuable information on the performance of the experiment and can thereby guide further decisions on experimental design. Solexa/Illumina deep sequencing is the technology of choice if interest lies in genes expressed in the low-intensity range. Researchers can get guidance on experimental design using our approach on their own pilot data implemented as a BioConductor package, SSPA http://bioconductor.org/packages/release/bioc/html/SSPA.html.}, author = {van Iterson, M. and 't Hoen, P. A. and Pedotti, P. and Hooiveld, G. J. and den Dunnen, J. T. and van Ommen, G. J. and Boer, J. M. and Menezes, R. X.}, citeulike-article-id = {5801492}, citeulike-linkout-0 = {http://dx.doi.org/10.1186/1471-2164-10-439}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/19758461}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=19758461}, doi = {10.1186/1471-2164-10-439}, issn = {1471-2164}, journal = {BMC genomics}, keywords = {analysis, data, expression, gene, power, profiling, relative, sample, size}, number = {1}, pages = {439+}, posted-at = {2009-10-12 11:29:48}, priority = {2}, title = {Relative power and sample size analysis on gene expression profiling data.}, url = {http://dx.doi.org/10.1186/1471-2164-10-439}, volume = {10}, year = {2009} }

TY - JOUR ID - citeulike:5801492 L3 - citeulike-article-id:5801492 N2 - BACKGROUND: With the increasing number of expression profiling technologies, researchers today are confronted with choosing the technology that has sufficient power with minimal sample size, in order to reduce cost and time. These depend on data variability, partly determined by sample type, preparation and processing. Objective measures that help experimental design, given own pilot data, are thus fundamental. RESULTS: Relative power and sample size analysis were performed on two distinct data sets. The first set consisted of Affymetrix array data derived from a nutrigenomics experiment in which weak, intermediate and strong PPARalpha agonists were administered to wild-type and PPARalpha-null mice. Our analysis confirms the hierarchy of PPARalpha-activating compounds previously reported and the general idea that larger effect sizes positively contribute to the average power of the experiment. A simulation experiment was performed that mimicked the effect sizes seen in the first data set. The relative power was predicted but the estimates were slightly conservative. The second, more challenging, data set describes a microarray platform comparison study using hippocampal deltaC-doublecortin-like kinase transgenic mice that were compared to wild-type mice, which was combined with results from Solexa/Illumina deep sequencing runs. As expected, the choice of technology greatly influences the performance of the experiment. Solexa/Illumina deep sequencing has the highest overall power followed by the microarray platforms Agilent and Affymetrix. Interestingly, Solexa/Illumina deep sequencing displays comparable power across all intensity ranges, in contrast with microarray platforms that have decreased power in the low intensity range due to background noise. This means that deep sequencing technology is especially more powerful in detecting differences in the low intensity range, compared to microarray platforms. CONCLUSION: Power and sample size analysis based on pilot data give valuable information on the performance of the experiment and can thereby guide further decisions on experimental design. Solexa/Illumina deep sequencing is the technology of choice if interest lies in genes expressed in the low-intensity range. Researchers can get guidance on experimental design using our approach on their own pilot data implemented as a BioConductor package, SSPA http://bioconductor.org/packages/release/bioc/html/SSPA.html. IS - 1 JF - BMC genomics SN - 1471-2164 TI - Relative power and sample size analysis on gene expression profiling data. VL - 10 SP - 439 KW - analysis KW - data KW - expression KW - gene KW - power KW - profiling KW - relative KW - sample KW - size AU - van Iterson, M AU - 't Hoen, PA AU - Pedotti, P AU - Hooiveld, GJ AU - den Dunnen, JT AU - van Ommen, GJ AU - Boer, JM AU - Menezes, RX PY - 2009/// UR - http://dx.doi.org/10.1186/1471-2164-10-439 ER -