This dataset describes mesenchymal stem cell response to BMP6 treatment. This is a typical small dataset with as few as two samples per condition like in most experimental studies. BMP6 treated samples and controls are one-on-one matched. This data has been extensively analyzed in GAGE paper, and was used as the primary demo data in earlier versions of gage package.
GSE16873 is a breast cancer study (Emery et al, 2009) downloaded from Gene Expression Omnibus (GEO). GSE16873 covers twelve patient cases, each with HN (histologically normal), ADH (ductal hyperplasia), and DCIS (ductal carcinoma in situ) RMA samples. Hence, there are 12*3=36 microarray hybridizations or samples interesting to us plus 4 others less interesting in the full dataset, gse16873.full. Dataset gse16873 in gage and gse16873.2 in this package are half datasets each with only HN and DCIS samples of 6 patients. Dataset gse16873.affyid is similar to gse16873 in gage package, except that row IDs are Affymetrix probe set IDs instead of Entrez Gene IDs. This is becuase Affymetrix original CDF (hgu133a) instead of Entrez Gene based on CDF was used when processing the raw data.
This dataset describes HeLa cell response to RNA-binding protein hnRNP C (HNRNPC) knock down. There are two replicate samples from each HNRNPC knockdown condition/siRNA (KD1 and KD2). In addition, there are four control HeLa cell samples. This is a typical RNA-seq dataset with two experimental groups. Experiment and control samples in this study should be treated as unpaired. This data is used as the primary demo data in the RNA-seq pathway analysis workflow of gage package.
These two data provide mapping between Entrez IDs, official symbols and ORF (open reading frame) IDs for budding yeast genes. These data are useful for yeast microarray data analysis. sc.gene is a 3-column matrix listing the Entrez IDs, official symbols and ORF (open reading frame) IDs for all known genes. orf2eg is a named vector mapping ORF IDs to Entrez IDs.
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