Computational protocol: Microarray platform consistency is revealed by biologically functional analysis of gene expression profiles

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Protocol publication

[…] The microarrays from the 4 platforms contain different numbers of probes for gene expression analysis. Specifically, 31099, 26857, 41071 and 35129 probes (or probe-set for AFX) are present in AFX, ABI, AG1 and GEH microarrays, respectively. According to Entrez gene ID, these probes correspond to 13713, 16280, 16135 and 12576 genes in AFX, ABI, AG1 and GEH microarrays, respectively. There are 5824 genes that are common across all 4 platforms. In contrast to the MAQC study that used the common genes for cross-platform comparison, we used the whole gene set of each platform to select DEGs. The data analysis was conducted using ArrayTrack software (http://www.fda.gov/nctr/science/centers/toxicoinformatics/ArrayTrack/index.htm). The gene expression data were normalized by using quantile method. Significance Analysis of Microarrays (SAM) was used to calculate q values. Two class unpaired analysis with 500 permutations was performed. DEGs were selected based on q < 0.01.Mock gene lists were created by randomly selecting genes for each platform or site to serve as negative controls for cross-platform comparison. To generate the control gene lists, every probe of a platform was assigned an integer number as ID. The probes were randomly chosen by ID. The number of genes randomly chosen from a platform/site is the same as the number in the DEG list. […]

Pipeline specifications

Software tools ArrayTrack, SAM
Databases Gene
Application Gene expression microarray analysis
Organisms Rattus norvegicus
Diseases Drug-Related Side Effects and Adverse Reactions