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Table 1 Latin Square experiment

From: SiPaGene: A new repository for instant online retrieval, sharing and meta-analyses of GeneChip® expression data

Group ID

Gene ID of spiked sequence

EXP 1

EXP 2

EXP 3

EXP 4

EXP 5

EXP 6

EXP 7

EXP 8

EXP 9

EXP 10

EXP 11

EXP 12

EXP 13

EXP 14

1

203508_at

204563_at

204513_s_at

0

0.125

0.25

0.5

1

2

4

8

16

32

64

128

256

512

2

204205_at

204959_at

207655_s_at

0.125

0.25

0.5

1

2

4

8

16

32

64

128

256

512

0

3

204836_at

205291_at

209795_at

0.25

0.5

1

2

4

8

16

32

64

128

256

512

0

0.125

4

207777_s_at

204912_at

205569_at

0.5

1

2

4

8

16

32

64

128

256

512

0

0.125

0.25

5

207160_at

205692_s_at

212827_at

1

2

4

8

16

32

64

128

256

512

0

0.125

0.25

0.5

6

209606_at

205267_at

204417_at

2

4

8

16

32

64

128

256

512

0

0.125

0.25

0.5

1

7

205398_s_at

209734_at

209354_at

4

8

16

32

64

128

256

512

0

0.125

0.25

0.5

1

2

8

206060_s_at

205790_at

200665_s_at

8

16

32

64

128

256

512

0

0.125

0.25

0.5

1

2

4

9

207641_at

207540_s_at

204430_s_at

16

32

64

128

256

512

0

0.125

0.25

0.5

1

2

4

8

10

203471_s_at

204951_at

207968_s_at

32

64

128

256

512

0

0.125

0.25

0.5

1

2

4

8

16

11

AFFX-r2-TagA_at

AFFX-r2-TagB_at

AFFX-r2-TagC_at

64

128

256

512

0

0.125

0.25

0.5

1

2

4

8

16

32

12

AFFX-r2-TagD_at

AFFX-r2-TagE_at

AFFX-r2-TagF_at

128

256

512

0

0.125

0.25

0.5

1

2

4

8

16

32

64

13

AFFX-r2-TagG_at

AFFX-r2-TagH_at

AFFX-DapX-3_at

256

512

0

0.125

0.25

0.5

1

2

4

8

16

32

64

128

14

AFFX-LysX-3_at

AFFX-PheX-3_at

AFFX-ThrX-3_at

512

0

0.125

0.25

0.5

1

2

4

8

16

32

64

128

256

  1. Concentrations (pmol) of spiked sequences for all 14 experiments. Details and sequences are presented on the Affymetrix web site [28]. Seven of the 42 spikes affect 23 additional probe sets of the HG-U133Atag array, thus increasing the number of affected probe sets on the HG-U133Atag array to 65. The spike for probe set 205398_s_at in group 7 consists of sequence elements identical to 5 of the 11 oligonucleotides of probe set 205397_x_at. Thus, comparing experiment 8 with all other experiments has the best chance to detect interference with probe set 205397_x_at (Figure 5). The sequences spiked in group 14 interfere with the here shown 3 and 15 additional probe sets. This spike group has the lowest concentrations in experiments two to six (0 to 1.0 pmol), resulting in the lowest recall rates in these comparisons (cf. figure 4, chart number 2 – 6). In these comparisons not only 3 but 18 true positives have very low concentrations and are difficult to detect.