Colantuoni2011_PFC_dev.RdSummarizedExperiment Objects including data used in Isildak et al 2020 paper analyzing age-related gene expression heterogeneity.
Colantuoni2011_PFC_dev
38 SummarizedExperiment objects of varying dimensions. RMA correction (using the ‘oligo’ library in R) and log2 transformation were applied to Somel2011 and Kang2011 datasets. For the Colantuoni2011 dataset, as there was no public R package to analyze the raw data, we used the preprocessed data deposited in GEO, which had been loess normalized by the authors. We applied a correction procedure for Somel2011 datasets, in which there was a batch effect influencing the expression levels, as follows: for each probeset (1) calculate mean expression (M), (2) scale each batch separately (to mean = 0, standard deviation = 1), (3) add M to each value. We excluded outliers given in Supplementary Table S1 of the paper, through a visual inspection of the first two principal components for the probeset expression levels. Objects are named as "DataSource_BrainRegion_Period", where the period is either development (dev; 0-20 years of age) or aging (age; 20+ years of age). All data are quantile normalized.
https://www.biorxiv.org/content/10.1101/595249v4 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30272 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE25219 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22569 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18069