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Preferred analysis methods for Affymetrix GeneChips. II. An expanded, balanced, wholly-defined spike-in dataset

ABSTRACT: We present a new wholly defined Affymetrix spike-in dataset consisting of 18 microarrays. Over 5700 RNAs are spiked in at relative concentrations ranging from 1- to 4-fold, and the arrays from each condition are balanced with respect to both total RNA amount and degree of positive- versus negative-fold change. We use this new â??Platinum Spikeâ?? dataset to evaluate microarray analysis routes and contrast the results to those achieved using our earlier Golden Spike dataset. PCR products from 5725 Drosophila Gene Collection release 1.0 (DGCr1) cDNA clones were collected into 28 distinct pools, and three independent in vitro transcription and labeling reactions were performed for each pool. Labeled cRNAs from each individual pool were then added at specified amounts to samples A and B to achieve the desired fold change differences between samples. 24 cRNAs generated from DGCr2 cDNA clones were added to each sample in known concentrations before hybridization.

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Marc Halfon 

PROVIDER: E-GEOD-21344 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Preferred analysis methods for Affymetrix GeneChips. II. An expanded, balanced, wholly-defined spike-in dataset.

Zhu Qianqian Q   Miecznikowski Jeffrey C JC   Halfon Marc S MS  

BMC bioinformatics 20100527

<h4>Background</h4>Concomitant with the rise in the popularity of DNA microarrays has been a surge of proposed methods for the analysis of microarray data. Fully controlled "spike-in" datasets are an invaluable but rare tool for assessing the performance of various methods.<h4>Results</h4>We generated a new wholly defined Affymetrix spike-in dataset consisting of 18 microarrays. Over 5700 RNAs are spiked in at relative concentrations ranging from 1- to 4-fold, and the arrays from each condition  ...[more]

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