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Table 1 Summary of data sets and corresponding collapsing strategies

From: Strategies for aggregating gene expression data: The collapseRows R function

Fig Analysis Data sets used 1. max 2. var 3. kMax 4. kVar 5. ME 6. Avg
1 Summary Hypothetical data X - X - - -
2 Collapsing probes to genes 18 Human Brain # 20 Mouse Brain % 5 Human Blood $ X X X X - -
3 Choosing module centroids 7 Human Brain # 8 Mouse Brain % 5 Human Blood $ X - X - X -
4 Predicting cell type proportions Abbas et al 2009 (cell lines) X - X - X X
5 Predicting cell type proportions Grigoryev et al 2010 (whole blood) X - X - X X
  1. "#" - The 18 human brain data sets were the following GSE numbers: 1133, 1297, 1572, 2164B, 3526A, 3526B, 3790A, 3790B, 3790C, 4036, 4757, 5281A, 5281B, 5388A, 5388B, 7621, 8397, and 9770. "%" - The 20 mouse brain data sets were the following GSE numbers: 1482, 1782A, 1782B, 2392, 3248, 3327A, 3327B, 3594C, 3963A, 3963B, 4269, 4734, 5429, 6285, 6514A, 6514B, 9444A, 9444B, 9444C, 10263. For "#" and "&," underlined data sets were used in Figure 3 as well as Figure 2. See Miller et al 2010 for more details on these data sets. "$" - The 5 human blood data sets were from Dumeaux et al 2010, Goring et al 2007, Pankla et al 2009, and Saris et al 2009.