Data files and supplementary information for Affymetrix – Illumina comparison

Supplement to Experimental comparison and cross-validation of the Affymetrix and Illumina gene expression analysis platforms.
Barnes M, Freudenberg J, Thompson S, Aronow B, Pavlidis P pubmed reprint


The growth in popularity of RNA expression microarrays has been accompanied by concerns about the reliability of the data especially when comparing between different platforms. Here, we present an evaluation of the reproducibility of microarray results using two platforms, Affymetrix GeneChips and Illumina BeadArrays. The study design is based on a dilution series of two human tissues (blood and placenta), tested in duplicate on each platform. The results of a comparison between the platforms indicate very high agreement, particularly for genes which are predicted to be differentially expressed between the two tissues. Agreement was strongly correlated with the level of expression of a gene. Concordance was also improved when probes on the two platforms could be identified as being likely to target the same set of transcripts of a given gene. These results shed light on the causes or failures of agreement across microarray platforms. The set of probes we found to be most highly reproducible can be used by others to help increase confidence in analyses of other data sets using these platforms.



Supplementary figures


Data files

The data files for all microarrays are available from GEO under accession number GSE3077.


For the affymetrix data, the original raw data files (e.g., CEL files) are available on the GEO site.


For the Illumina data, the “rawest” data we have is here. This includes some extra summary statistics for each probe on each array, but not the individual bead intensity values. The individual bead values were not retained by the Illumina analysts. The “mean” values in that file corresponds to the values used as a starting point in our analysis.


The following files were used in the analyses presented in the paper: