Competition results: Table 10

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 10. hgu95a entries ranked by: Obs-(low)int-fc slope

(*: #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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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 10. hgu133 entries ranked by: Obs-(low)int-fc slope

(^: #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
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
84 plier / zhongxue 0.20 0.24 4.28 0.85 0.82 0.91 0.75 0.75 0.82 0.91 0.27 0.05 0.07 0.22
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
90 lmc3 / fasold 0.30 0.45 2.62 0.92 1.04 0.60 1.06 1.09 1.04 0.78 0.27 0.12 0.16 0.23
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
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
52 Afit_fn / Michael.D.Lynch 0.18 0.17 0.79 0.87 0.86 0.55 0.85 0.82 0.86 0.67 0.61 0.74 0.73 0.64
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
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
74 HLehmann / mhossain 0.30 0.42 3.67 0.91 0.75 0.53 0.72 0.77 0.75 0.59 0.08 0.00 0.00 0.06
59 DQN / wei-min.liu 0.24 0.35 2.21 0.93 0.76 0.48 0.76 0.72 0.76 0.57 0.22 0.03 0.05 0.17
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
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
82 gcrma / zhongxue 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
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
85 OLIGO / stephan.preibisch 0.56 0.59 19.14 0.67 1.32 2.17 1.01 1.18 1.32 2.18 0.10 0.00 0.00 0.07
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
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
69 chipcal4 / mahoney.douglas 0.10 0.21 0.82 0.82 0.95 0.31 0.87 1.64 0.95 0.42 0.44 0.76 0.96 0.52
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
86 cl081406 / cli 0.15 0.26 3.04 0.92 0.69 0.29 0.74 0.69 0.69 0.39 0.03 0.00 0.00 0.02
78 NLF_test / scvortso 0.00 0.00 1.00 0.89 0.74 0.29 0.71 1.11 0.74 0.38 0.71 0.78 0.86 0.73
79 NLF_bior / scvortso 0.00 0.00 0.00 0.89 0.74 0.29 0.71 1.11 0.74 0.38 0.92 0.97 0.98 0.93
80 NLF_bior / scvortso 0.00 0.00 0.00 0.89 0.74 0.29 0.71 1.11 0.74 0.38 0.89 0.94 0.96 0.90
77 Dimo2 / mena2 0.12 0.17 0.57 0.90 0.79 0.25 0.83 0.97 0.79 0.35 0.52 0.88 0.94 0.61
70 rse / jack.liu 0.14 0.20 2.03 0.91 0.64 0.27 0.65 0.80 0.64 0.35 0.09 0.04 0.12 0.08
62 l-FARMS / hochreit 0.00 0.00 0.08 0.90 1.02 0.23 1.04 1.49 1.02 0.33 0.91 0.99 1.00 0.93
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
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
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
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
87 test / cresus22 0.07 0.13 0.41 0.89 0.65 0.22 0.67 0.79 0.64 0.29 0.56 0.90 0.92 0.64
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
68 RMA-75 / mmcgee 0.08