Table 2

Contents of an exemplary “sample_info.txt” file Batch Covariate
1 GSM574058 GSM574058 GSE23402 fibroblast
2 GSM574059 GSM574059 GSE23402 fibroblast
3 GSM574060 GSM574060 GSE23402 fibroblast
4 GSM574061 GSM574061 GSE23402 ESC
5 GSM574062 GSM574062 GSE23402 ESC
6 GSM574063 GSM574063 GSE23402 ESC
7 GSM574064 GSM574064 GSE23402 ESC
8 GSM574065 GSM574065 GSE23402 ESC
9 GSM574066 GSM574066 GSE23402 ESC
10 GSM574067 GSM574067 GSE23402 ESC
11 GSM574068 GSM574068 GSE23402 ESC
12 GSM574069 GSM574069 GSE23402 ESC
13 GSM574070 GSM574070 GSE23402 ESC
14 GSM574071 GSM574071 GSE23402 ESC
15 GSM574072 GSM574072 GSE23402 ESC
16 GSM574073 GSM574073 GSE23402 ESC
17 GSM574074 GSM574074 GSE23402 ESC
18 GSM574075 GSM574075 GSE23402 ESC
19 GSM574076 GSM574076 GSE23402 ESC
20 GSM574077 GSM574077 GSE23402 ESC
21 GSM574078 GSM574078 GSE23402 iPSC
22 GSM574079 GSM574079 GSE23402 iPSC
23 GSM574080 GSM574080 GSE23402 iPSC
24 GSM574081 GSM574081 GSE23402 iPSC
25 GSM648497 GSM648497 GSE26428 iPSC
26 GSM648498 GSM648498 GSE26428 iPSC
27 GSM648499 GSM648499 GSE26428 fibroblast
28 GSM710513 GSM710513 GSE28688 fibroblast
29 GSM710514 GSM710514 GSE28688 fibroblast
30 GSM710515 GSM710515 GSE28688 fibroblast
31 GSM710516 GSM710516 GSE28688 fibroblast
32 GSM710517 GSM710517 GSE28688 fibroblast
33 GSM710518 GSM710518 GSE28688 fibroblast
34 GSM710519 GSM710519 GSE28688 fibroblast
35 GSM710520 GSM710520 GSE28688 fibroblast
36 GSM710521 GSM710521 GSE28688 ESC
37 GSM710522 GSM710522 GSE28688 ESC
38 GSM710523 GSM710523 GSE28688 iPSC
39 GSM710524 GSM710524 GSE28688 iPSC
40 GSM710525 GSM710525 GSE28688 iPSC
41 GSM710526 GSM710526 GSE28688 iPSC

The first two columns need to correspond to the sample names used in the ExpressionSets, respectively. In column 3 the contribution of individual samples to batches is tracked. Finally, column 4 contains user defined group assignments of each sample. Group assignments (covariates) can include more than one column, for example to include source tissue, sex, age, etc.

Heider and Alt

Heider and Alt BMC Bioinformatics 2013 14:75   doi:10.1186/1471-2105-14-75

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