PreP+07: improvements of a user friendly tool to preprocess and analyse microarray data

BMC Bioinformatics

Table 3 Differentially expressed genes obtained with the FL protocol using PreP+07 contrasting their rank-position against Limma ranking.

[1] ID	[2] P+07 pvalue	[3] P+07 rank	[4] R pvalue	[5] R rank	[6] pvalue difference
2108	4.92E-04	1	5.54E-04	1	6.20E-05
8057	0.00277	2	8.91E-04	2	1.88E-03
269	0.00318	3	3.259E-03	3	7.75E-05
3677	0.00376	4	0.00845	9	0.00469
8708	0.00408	5	0.00384	6	0.00024
6174	0.00661	6	0.01569	25	0.00908
11844	0.00665	7	0.00378	5	0.00287
10247	0.00738	8	0.03051	61	0.02312
9724	0.00831	9	0.01275	19	0.00444
1783	0.00907	10	0.00980	12	0.00072
10585	0.00952	11	0.01106	14	0.00153
2213	0.00997	12	0.02626	46	0.01628

Columns correspond to: [1] gene ID; [2] and [4] t-test p-value for data processed by PreP (in increasing order) and Limma; [3] and [5] position in the list of significant genes in PreP+07 and Limma; [6] differences in p-value: | [2] – [4] |. T-test p-values were obtained using MeV from TM4 package.

ISSN: 1471-2105