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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.
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BMC Bioinformatics

ISSN: 1471-2105

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