Assessing the quality of hybridized RNA in Affymetrix GeneChips using linear regression. Export

@article{citeulike:4306474, abstract = {The quality of data from microarray analysis is highly dependent on the quality of RNA. Because of the lability of RNA, steps involved in tissue sampling, RNA purification, and RNA storage are known to potentially lead to the degradation of RNAs; therefore, assessment of RNA quality and integrity is essential. Existing methods for estimating the quality of RNA hybridized to a GeneChip either suffer from subjectivity or are inefficient in performance. To overcome these drawbacks, we propose a linear regression method for assessing RNA quality for a hybridized Genechip. In particular, our approach used the probe intensities from the .cel files that the Affymetrix software associates with each microarray. The effectiveness and the improvements of the proposed method over the existing methods are illustrated by the application of the method to the previously published 19 human Affymetrix microarray data sets for which external verification of RNA quality is available.}, author = {Li, Meijuan and Reilly, Cavan}, citeulike-article-id = {4306474}, citeulike-linkout-0 = {http://view.ncbi.nlm.nih.gov/pubmed/19137095}, citeulike-linkout-1 = {http://www.hubmed.org/display.cgi?uids=19137095}, issn = {1943-4731}, journal = {Journal of biomolecular techniques : JBT}, keywords = {affy, quality\_control, rna\_quality}, month = {April}, number = {2}, pages = {122--128}, posted-at = {2009-04-14 11:29:44}, priority = {4}, title = {Assessing the quality of hybridized RNA in Affymetrix GeneChips using linear regression.}, url = {http://view.ncbi.nlm.nih.gov/pubmed/19137095}, volume = {19}, year = {2008} }

TY - JOUR ID - citeulike:4306474 L3 - citeulike-article-id:4306474 N2 - The quality of data from microarray analysis is highly dependent on the quality of RNA. Because of the lability of RNA, steps involved in tissue sampling, RNA purification, and RNA storage are known to potentially lead to the degradation of RNAs; therefore, assessment of RNA quality and integrity is essential. Existing methods for estimating the quality of RNA hybridized to a GeneChip either suffer from subjectivity or are inefficient in performance. To overcome these drawbacks, we propose a linear regression method for assessing RNA quality for a hybridized Genechip. In particular, our approach used the probe intensities from the .cel files that the Affymetrix software associates with each microarray. The effectiveness and the improvements of the proposed method over the existing methods are illustrated by the application of the method to the previously published 19 human Affymetrix microarray data sets for which external verification of RNA quality is available. IS - 2 JF - Journal of biomolecular techniques : JBT SN - 1943-4731 EP - 128 TI - Assessing the quality of hybridized RNA in Affymetrix GeneChips using linear regression. VL - 19 SP - 122 KW - affy KW - quality_control KW - rna_quality AU - Li, Meijuan AU - Reilly, Cavan PY - 2008/04// UR - http://view.ncbi.nlm.nih.gov/pubmed/19137095 ER -