Validating Cell Deconvolution Signatures

Three external datasets were collected to validate our signature matrices (for RNA-Seq and microarray deconvolution) (Figure S9). 1) The dataset from Zimmermann et al. (2016) (link) provides both flow cytometry data and RNA-Seq data and the data are available through ImmPort (http://www.immport.org) with accession number SDY67. Cell types proportions were retrieved from their B cell, T regs and innate flow cytometry panels. 2) The dataset from Newman et al. (2015) (link) was downloaded from GEO: GSE65133. The dataset provides both microarray data and cell type proportions. 3) For the dataset of Mohanty et al. (2015) (link), we downloaded the microarray data from GEO: GSE9654, and flow cytometry data from ImmPort, accession number SDY404. We analyzed the T cells and B cells panels (L1 and L4, respectively).
The three external datasets contain both PBMC transcriptomic data and flow cytometry data where cell type proportions can be obtained in relation to the PBMC fraction of blood. All the flow cytometry proportion extracted are available in Table S6.