The gene set analysis software was compared using three datasets including two large studies and one small one.
The two large studies included a lung cancer set was provided with GSEA-R package [49 ] and a type 2 diabetes dataset comes from ChipperDB [51 ]. These datasets were chosen because they were originally used to validate and/or compare GSEA [3 (link),4 (link)] and PAGE [5 (link)]
The small dataset is a gene expression study from our group describing human MSC response to 8 hours of exposure to the signaling molecule BMP6. This dataset includes two experimental groups each with paired treatment and control samples, resulting in a total of 4 gene chips. We have deposited the dataset into Gene Expression Omnibus (GEO) repository (accession number GSE13604). For the use in this paper, the raw data were processed by using RMA implemented in the Bioconductor Affy package [52 (link)] with up-to-date probe set definition (.CDF file) based on Entrez Gene sequence, Hs133P_Hs_ENTREZG_8 [53 (link)]. Annotation data were retrieved from the GAIQ website [48 ]. The type 2 diabetes dataset was processed similarly from raw data files.
The two large studies included a lung cancer set was provided with GSEA-R package [49 ] and a type 2 diabetes dataset comes from ChipperDB [51 ]. These datasets were chosen because they were originally used to validate and/or compare GSEA [3 (link),4 (link)] and PAGE [5 (link)]
The small dataset is a gene expression study from our group describing human MSC response to 8 hours of exposure to the signaling molecule BMP6. This dataset includes two experimental groups each with paired treatment and control samples, resulting in a total of 4 gene chips. We have deposited the dataset into Gene Expression Omnibus (GEO) repository (accession number GSE13604). For the use in this paper, the raw data were processed by using RMA implemented in the Bioconductor Affy package [52 (link)] with up-to-date probe set definition (.CDF file) based on Entrez Gene sequence, Hs133P_Hs_ENTREZG_8 [53 (link)]. Annotation data were retrieved from the GAIQ website [48 ]. The type 2 diabetes dataset was processed similarly from raw data files.
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