Competition results: Table 0

Table95a (resp. Table133) below displays a 14-dimensional score for each entry with a hgu95a (resp. hgu133) dataset. The score is a limited representation of our assessment, e.g. MAS 5.0. Entries are (or should be) uniquely identified by method and the e-mail address (account@host) of the submitter, but the tables use abbreviated identifiers, which should suffice, built from the method nickname and e-mail account. For details about a particular entry, click on its identifier.

Because of space considerations, the tables contain only a certain 14 of the 48 measures made by the assessment, and the measures displayed are rounded to 2 decimal places.

Ideal score values are included in italics. The current best score values are in bold italics.

To see the entries ranked with respect to a particular measure, click on the corresponding heading: "1" ... "14".

The score components, along with the corresponding assessment score number, are as follows:

  1. [26] Median SD - median SD across replicates
  2. [18] null log-fc IQR - Inter-quartile range of the log-fold-changes from genes that should not change.
  3. [20] null log-fc 99.9% - 99.9% percentile of the log-fold-changes if from the genes that should not change.
  4. [2] Signal detect R2 - R-squared obtained from regressing expression values on nominal concentrations in the spike-in data
  5. [1] Signal detect slope - slope obtained from regressing expression values on nominal concentrations in the spike-in data
  6. [29] low.slope - Slope from regression of observed log concentration versus nominal log concentraion for genes with low intensities.
  7. [30] med.slope - As above but for genes with medium intensities.
  8. [31] high.slope - As above but for genes with high intensities.
  9. [10] Obs-intended-fc slope - slope obtained from regressing observed log-fold-changes against nominal log-fold-changes
  10. [11] Obs-(low)int-fc slope - slope obtained from regressing observed log-fold-changes against nominal log-fold-changes for genes with nominal concentrations less than or equal to 2.
  11. [21] low AUC - Area under the ROC curve (up to 100 false positives) for genes with low intensity standardized so that optimum is 1.
  12. [22] med AUC - As above but for genes with medium intensities.
  13. [23] high AUC - As above but for genes with high intensities.
  14. [24] weighted avg AUC - A weighted average of the previous 3 ROC curves with weights related to amount of data in each class (low,medium,high).

Table 0. hgu95a entries listed in order of submission

(*: #genes subnormal)

N Method / Submitter 1 2 3 4 5 6 7 8 9 10 11 12 13 14
0 (perfection) 0.00 0.00 0.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00
1 MAS_5.0 / rafa 0.63 0.85 4.48 0.86 0.71 0.72 0.80 0.45 0.69 0.65 0.07 0.00 0.00 0.05
2 RMA / rafa 0.11 0.19 0.57 0.80 0.63 0.29 0.73 0.47 0.61 0.36 0.51 0.91 0.64 0.60
3 dChip / rafa 0.13 0.20 1.44 0.85 0.53 0.25 0.64 0.39 0.52 0.32 0.21 0.43 0.16 0.26
4 ZAM2NBG / magnus.astrand 0.09 0.16 0.50 0.77 0.57 0.25 0.66 0.47 0.57 0.32 0.57 0.95 0.74 0.66
5 qn.p5 / cope 0.12 0.22 1.09 0.50 0.42 0.11 0.44 0.52 0.43 0.14 0.09 0.43 0.46 0.17
6 vsn_scal / w.huber 0.09 0.15 0.43 0.81 0.77 0.21 0.82 0.70 0.75 0.28 0.53 0.97 0.86 0.64
7 vsn / w.huber 0.06 0.10 0.29 0.81 0.51 0.14 0.55 0.47 0.50 0.19 0.53 0.97 0.86 0.64
8 RMAVSN / thomas.cappola 0.09 0.16 0.48 0.81 0.61 0.25 0.71 0.46 0.60 0.32 0.52 0.94 0.70 0.62
9 RMA_NBG / bolstad 0.04 0.08 0.24 0.81 0.48 0.12 0.50 0.46 0.47 0.15 0.55 0.97 0.92 0.65
10 GSVDmin / hzuzan 0.08 0.13 0.60 0.83 0.50 0.17 0.58 0.41 0.49 0.24 0.39 0.87 0.65 0.51
11 PLIER / Earl Hubbell 0.19 0.33 123.27 0.91 0.71 0.76 0.84 0.46 0.72 0.65 0.04 0.00 0.00 0.03
12 GSVDmod / hzuzan 0.07 0.13 0.44 0.85 0.51 0.18 0.60 0.42 0.50 0.24 0.47 0.94 0.74 0.59
13 PLIER+16 / Earl Hubbell 0.13 0.21 0.83 0.91 0.65 0.45 0.78 0.46 0.65 0.46 0.61 0.83 0.46 0.66
14 GCRMA / zwu 0.09 0.16 0.77 0.84 0.97 0.73 1.19 0.55 0.92 0.66 0.62 0.94 0.59 0.69
15 ChipMan / plauren 0.27 0.33 2.26 0.82 0.88 0.36 1.04 0.68 0.87 0.44 0.21 0.50 0.24 0.28
16 ProbePro / shilmer 0.31 0.47 18.75 0.47 1.45 1.26 1.73 0.39 1.33 1.93 0.05 0.04 0.00 0.05
17 MMEI / shibing.deng 0.04 0.06 0.23 0.80 0.45 0.11 0.49 0.46 0.45 0.16 0.57 0.98 0.94 0.67
18 PM / zhangli * 0.05 0.09 0.40 0.87 0.46 0.14 0.52 0.43 0.45 0.18 0.47 0.93 0.83 0.59
19 RMA:GNV / szeto 0.11 0.19 0.58 0.80 0.62 0.29 0.73 0.47 0.61 0.36 0.50 0.91 0.64 0.60
20 GL / mai98ftu 0.05 0.08 0.25 0.81 0.48 0.12 0.50 0.46 0.47 0.16 0.58 0.96 0.88 0.67
21 MAS5+32 / Earl Hubbell 0.14 0.23 1.07 0.88 0.60 0.31 0.68 0.44 0.59 0.33 0.04 0.28 0.08 0.10
22 gMOS_v.1 / m.milo 0.29 0.00 3.35 0.75 0.95 0.82 1.22 0.42 0.94 1.04 0.07 0.04 0.00 0.06
23 rsvd / jack liu 0.00 0.00 0.58 0.90 0.66 0.31 0.84 0.40 0.66 0.41 0.54 0.93 0.54 0.64
24 ZL / lzhou 0.22 0.12 0.52 0.65 0.57 0.39 0.67 0.45 0.57 0.36 0.65 0.87 0.73 0.70
32 gltran / lzhou 0.07 0.12 0.42 0.78 0.51 0.19 0.57 0.45 0.50 0.22 0.55 0.94 0.80 0.65
33 UM-Tr-Mn / jmacdon 0.32 0.51 2.92 0.87 0.68 0.53 0.82 0.42 0.67 0.54 0.11 0.00 0.00 0.08
34 GS_RMA / thon 0.11 0.19 0.57 0.80 0.63 0.29 0.73 0.47 0.61 0.36 0.51 0.91 0.64 0.60
35 GS_GCRMA / thon 0.10 0.07 0.79 0.91 0.84 0.51 1.02 0.55 0.82 0.65 0.64 0.94 0.56 0.72
36 gcrma113 / zwu 0.08 0.04 0.74 0.91 0.87 0.52 1.06 0.56 0.86 0.68 0.68 0.97 0.63 0.75
41 mgMOS_gs / liux 0.36 0.55 2.86 0.82 0.76 0.77 0.89 0.43 0.75 0.90 0.25 0.04 0.00 0.20
42 mmgMOSgs / liux 0.40 0.58 3.27 0.80 1.03 1.21 1.26 0.45 1.02 1.40 0.36 0.07 0.00 0.29
43 vsn / huber 0.06 0.10 0.28 0.81 0.51 0.14 0.54 0.46 0.50 0.18 0.53 0.97 0.86 0.64
44 vsn_scal / huber 0.09 0.15 0.42 0.81 0.76 0.21 0.82 0.70 0.74 0.28 0.53 0.97 0.86 0.64
49 dChipwMM / rafa 0.32 0.38 10.83 0.61 0.91 0.78 0.97 0.34 0.87 1.68 0.10 0.00 0.00 0.08
50 NLF95 / scvortso 0.00 0.00 0.00 0.89 0.65 0.25 0.68 0.68 0.64 0.34 0.74 0.92 0.95 0.79
53 Afit_qn / Michael.D.Lynch 0.07 0.00 1.18 0.82 0.79 0.62 0.88 0.50 0.75 0.66 0.62 0.70 0.32 0.64
54 Afit_fn / Michael.D.Lynch 0.39 0.15 1.20 0.80 0.79 0.65 0.91 0.49 0.75 0.68 0.59 0.64 0.33 0.60
56 PQN / wei-min.liu 0.11 0.19 0.75 0.83 0.57 0.26 0.66 0.45 0.56 0.33 0.39 0.80 0.47 0.49
57 PQNB1 / wei-min.liu 0.02 0.03 0.11 0.78 0.08 0.05 0.11 0.04 0.08 0.07 0.50 0.71 0.14 0.55
58 PQNB1+16 / wei-min.liu 0.00 0.00 0.01 0.81 0.01 0.00 0.01 0.00 0.01 0.01 0.48 0.83 0.37 0.56
59 DQN / wei-min.liu 0.47 0.68 2.59 0.88 0.72 0.68 0.87 0.41 0.71 0.68 0.23 0.01 0.00 0.18
60 DQNB1 / wei-min.liu 0.05 0.08 0.27 0.84 0.08 0.09 0.09 0.04 0.07 0.10 0.35 0.06 0.00 0.28
61 DQNB1+16 / wei-min.liu 0.00 0.01 0.02 0.87 0.01 0.01 0.01 0.00 0.01 0.01 0.38 0.17 0.01 0.33
62 l-FARMS / hochreit 0.00 0.00 0.19 0.80 0.77 0.21 0.90 0.78 0.80 0.31 0.80 0.95 0.94 0.84
63 q-FARMS / hochreit 0.00 0.00 0.10 0.78 0.59 0.15 0.68 0.59 0.60 0.23 0.89 0.97 0.97 0.91
65 DIMO / mena2 0.24 0.33 3.10 0.80 0.87 0.52 1.13 0.45 0.85 0.72 0.27 0.36 0.04 0.29
67 RMA-Mean / mmcgee 0.11 0.19 0.73 0.81 0.59 0.25 0.67 0.47 0.58 0.31 0.40 0.82 0.51 0.50
68 RMA-75 / mmcgee 0.12 0.20 0.72 0.81 0.59 0.26 0.68 0.47 0.58 0.32 0.42 0.82 0.52 0.51
69 chipcal4 / mahoney.douglas 0.18 0.26 1.17 0.70 0.94 0.38 0.99 1.04 0.95 0.41 0.36 0.80 0.77 0.47
71 i_gcrma1 / Xu 0.09 0.06 0.79 0.91 0.84 0.51 1.02 0.55 0.82 0.65 0.64 0.94 0.57 0.72
72 i_gcrma2 / Xu 0.09 0.08 0.85 0.91 0.90 0.54 1.09 0.59 0.88 0.70 0.64 0.95 0.57 0.72
73 i_gcrma3 / Xu 0.08 0.06 0.79 0.91 0.84 0.51 1.02 0.55 0.82 0.66 0.65 0.95 0.57 0.72
76 dimo / mena2 0.05 0.09 0.38 0.79 0.52 0.14 0.56 0.52 0.51 0.18 0.48 0.95 0.89 0.60
81 dfwfcb / zhongxue 0.00 0.00 0.00 0.63 0.31 0.09 0.32 0.26 0.29 0.12 1.00 1.00 1.00 1.00
88 en.FARMS / clevert 0.00 0.00 0.00 0.85 0.63 0.16 0.72 0.62 0.65 0.25 1.00 1.00 1.00 1.00
89 VST-RMA / dupan 0.04 0.07 0.23 0.80 0.49 0.12 0.51 0.46 0.47 0.15 0.54 0.96 0.93 0.64
0 (perfection) 0.00 0.00 0.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00
N Method / Submitter 1 2 3 4 5 6 7 8 9 10 11 12 13 14

Table 0. hgu133 entries listed in order of submission

(^: #genes subnormal)

N Method / Submitter 1 2 3 4 5 6 7 8 9 10 11 12 13 14
0 (perfection) 0.00 0.00 0.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00
1 MAS_5.0 / rafa 0.29 0.47 4.01 0.91 0.77 0.58 0.73 0.77 0.77 0.64 0.09 0.00 0.00 0.06
2 RMA / rafa 0.07 0.13 0.40 0.90 0.68 0.20 0.71 0.80 0.68 0.31 0.57 0.91 0.96 0.65
8 RMAVSN / thomas.cappola 0.02 0.04 0.15 0.89 0.12 0.06 0.13 0.10 0.12 0.08 0.46 0.59 0.43 0.49
23 rsvd / jack liu 0.14 0.12 0.73 0.94 0.74 0.31 0.78 0.73 0.74 0.43 0.53 0.73 0.71 0.58
25 rsvd.pm / jack liu 0.06 0.11 0.34 0.89 0.53 0.12 0.53 0.77 0.53 0.16 0.42 0.90 0.96 0.54
26 rma-tog / dgreco 0.07 0.13 0.40 0.90 0.68 0.20 0.71 0.80 0.68 0.31 0.57 0.91 0.96 0.65
27 rma-sep / dgreco 0.18 0.28 0.96 0.90 0.71 0.27 0.72 0.84 0.71 0.39 0.38 0.53 0.63 0.42
28 LW1 / dgreco 0.08 0.14 1.18 0.91 0.59 0.19 0.62 0.74 0.59 0.25 0.23 0.47 0.55 0.29
29 LW2 / dgreco 0.14 0.25 13.88 0.56 1.08 1.50 0.80 0.68 1.08 1.45 0.19 0.00 0.00 0.14
30 rsvd.bgc / jack liu 0.08 0.14 0.52 0.89 0.58 0.16 0.59 0.79 0.58 0.22 0.38 0.80 0.90 0.49
31 cor523 / cope 0.02 0.03 0.12 0.88 0.12 0.06 0.13 0.10 0.12 0.08 0.54 0.77 0.61 0.60
33 UM-Tr-Mn / jmacdon 0.15 0.25 1.86 0.93 0.70 0.36 0.72 0.70 0.70 0.44 0.18 0.10 0.10 0.16
34 GS_RMA / thon 0.07 0.13 0.40 0.90 0.68 0.20 0.71 0.80 0.68 0.30 0.56 0.91 0.96 0.65
35 GS_GCRMA / thon 0.07 0.09 0.65 0.93 0.93 0.37 0.96 0.96 0.93 0.55 0.59 0.87 0.90 0.66
36 gcrma113 / zwu 0.06 0.04 0.61 0.91 1.00 0.25 1.13 0.97 1.00 0.48 0.45 0.91 0.92 0.57
37 rsvd2 / jack.liu 0.17 0.28 1.74 0.91 0.75 0.46 0.74 0.81 0.75 0.52 0.29 0.16 0.21 0.26
38 W237 / dario.greco 0.02 0.04 0.17 0.87 0.12 0.05 0.13 0.10 0.12 0.07 0.35 0.54 0.39 0.39
39 RMA_NBG / bolstad 0.01 0.02 0.06 0.90 0.09 0.02 0.09 0.10 0.09 0.04 0.54 0.90 0.93 0.63
40 RMAVSN / thomas.cappola 0.02 0.04 0.15 0.89 0.12 0.06 0.13 0.10 0.12 0.08 0.46 0.59 0.43 0.49
41 mgMOS_gs / liux 0.24 0.34 2.02 0.92 0.81 0.58 0.78 0.77 0.81 0.68 0.33 0.08 0.12 0.27
42 mmgMOSgs / liux 0.24 0.34 2.71 0.89 1.03 0.88 0.98 0.79 1.03 1.05 0.37 0.02 0.01 0.28
43 vsn / huber 0.05 0.09 0.24 0.88 0.52 0.10 0.51 0.78 0.52 0.16 0.53 0.93 0.99 0.63
44 vsn_scal / huber 0.07 0.13 0.36 0.88 0.78 0.15 0.77 1.16 0.78 0.23 0.53 0.93 0.99 0.63
45 NLF / scvortso 0.12 0.18 1.79 0.86 0.70 0.21 0.67 1.10 0.70 0.28 0.20 0.31 0.59 0.23
46 real / scvortso 0.05 0.02 0.51 0.00 -0.01 -0.06 -0.02 0.06 -0.01 -0.00 0.55 0.40 0.42 0.51
47 real / scvortso 0.05 0.02 0.53 0.90 1.04 0.09 1.34 0.97 1.04 0.30 0.33 0.95 0.93 0.48
48 NLF / scvortso 0.02 0.01 0.15 0.85 0.70 0.22 0.69 1.07 0.70 0.29 0.76 0.95 0.97 0.81
49 dChipwMM / rafa 0.20 0.26 9.61 0.65 0.98 1.13 0.81 0.69 0.99 1.17 0.19 0.00 0.00 0.14
51 Afit_qn / Michael.D.Lynch 0.06 0.03 0.74 0.87 0.86 0.55 0.86 0.82 0.86 0.66 0.61 0.78 0.79 0.65
52