Identifying technical aliases in SELDI mass spectra of complex mixtures of proteins

Whitin, John C; Rangan, Srinivasa; Cohen, Harvey J

doi:10.1186/1756-0500-6-358

BMC Research Notes

Table 2 Randomization test of technical clustering software

From: Identifying technical aliases in SELDI mass spectra of complex mixtures of proteins

Threshold	Original cluster	Weight	Cluster after randomizing Fx4_CM10_high_C066628	Weight
0.15	Fx4_CM10_high_C066628_	0.581	Not clustered	NA
	Fx4_CM10_high_C033359_	0.419
0.20	Fx4_CM10_high_C0133296	0.288	Not clustered	NA
	Fx4_CM10_high_C066628_	0.260
	Fx4_CM10_high_C033359_	0.176
	Fx3_CM10_high_C033347_	0.129
	Fx4_CM10_high_C022248_	0.061
	Fx3_CM10_high_C066617_	0.053
	Fx3_CM10_high_C022244_	0.033
0.25	Fx4_CM10_high_C0133296	0.250	Not clustered	NA
	Fx4_CM10_high_C066628_	0.230
	Fx4_CM10_high_C033359_	0.154
	Fx3_CM10_high_C033347_	0.121
	Fx3_CM10_high_C0133108	0.089
	Fx4_CM10_high_C022248_	0.055
	Fx3_CM10_high_C066617_	0.051
	Fx3_CM10_high_C022244_	0.027
	Fx4_H50_high_C022244_	0.024
0.3	Fx4_CM10_high_C0133296	0.238	Fx3_CM10_high_C033347_	0.237
	Fx4_CM10_high_C066628_	0.224	Fx4_CM10_high_C033359_	0.237
	Fx4_CM10_high_C033359_	0.151	Fx3_CM10_high_C0133108	0.152
	Fx3_CM10_high_C033347_	0.119	Fx4_CM10_high_C022248_	0.106
	Fx3_CM10_high_C0133108	0.087	Fx3_CM10_high_C066617_	0.093
	Fx4_CM10_high_C022248_	0.054	Fx5_H50_high_C022236_	0.065
	Fx3_CM10_high_C066617_	0.050	Fx4_CM10_high_C066628_	0.056
	Fx5_H50_high_C022236_	0.030	Fx3_CM10_high_C022244_	0.028
	Fx3_CM10_high_C022244_	0.026	Fx4_H50_high_C022244_	0.026
	Fx4_H50_high_C022244_	0.020
0.4	Fx4_CM10_high_C0133296	0.238	Fx4_CM10_high_C0133296	0.240
	Fx4_CM10_high_C066628_	0.224	Fx4_CM10_high_C033359_	0.165
	Fx4_CM10_high_C033359_	0.151	Fx3_CM10_high_C033347_	0.154
	Fx3_CM10_high_C033347_	0.119	Fx3_CM10_high_C0197893	0.117
	Fx3_CM10_high_C0133108	0.087	Fx3_CM10_high_C0133108	0.112
	Fx4_CM10_high_C022248_	0.054	Fx3_CM10_high_C066617_	0.065
	Fx3_CM10_high_C066617_	0.050	Fx4_CM10_high_C022248_	0.064
	Fx5_H50_high_C022236_	0.030	Fx5_H50_high_C022236_	0.036
	Fx3_CM10_high_C022244_	0.026	Fx3_CM10_high_C022244_	0.024
	Fx4_H50_high_C022244_	0.020	Fx4_H50_high_C022244_	0.012
			Fx4_CM10_high_C066628_	0.012
0.5	Fx4_CM10_high_C0133296	0.161	Fx4_CM10_high_C0133296	0.194
	Fx4_CM10_high_C066628_	0.140	Fx4_CM10_high_C0196854	0.155
	Fx4_CM10_high_C0196854	0.129	Fx4_CM10_high_C033359_	0.101
	Fx4_CM10_high_C033359_	0.088	Fx3_CM10_high_C033347_	0.074
	Fx3_CM10_high_C033347_	0.064	Fx3_CM10_high_C0197893	0.065
	Fx6_CM10_high_C033435_	0.060	Fx6_CM10_high_C033435_	0.065
	Fx3_CM10_high_C0197893	0.055	Fx3_CM10_high_C0133108	0.061
	Fx3_CM10_high_C0133108	0.052	Fx6_CM10_high_C066702_	0.042
	Fx6_CM10_high_C066702_	0.036	Fx6_CM10_high_C0133574	0.039
	Fx6_CM10_high_C0133574	0.033	Fx3_H50_high_C033429_	0.038
	Fx3_H50_high_C033429_	0.032	Fx4_CM10_high_C022248_	0.034
	Fx4_CM10_high_C022248_	0.030	Fx3_CM10_high_C066617_	0.033
	Fx3_CM10_high_C066617_	0.028	Fx3_H50_high_C066672_	0.023
	Fx3_H50_high_C066672_	0.019	Fx5_H50_high_C022236_	0.020
	Fx5_H50_high_C022236_	0.018	Fx3_H50_high_C0133496	0.019
	Fx3_CM10_high_C022244_	0.016	Fx3_CM10_high_C022244_	0.018
	Fx3_H50_high_C0133496	0.016	Fx4_H50_high_C022244_	0.017
	Fx4_H50_high_C022244_	0.013	Fx4_CM10_high_C066628_	0.002
	Fx5_CM10_high_C0133649	0.010
	Fx5_CM10_high_C066776_	0.001

The Technical Clustering software was applied to the dataset of spectra obtained from 85 samples before (left-hand column) and after (right hand column) randomizing the sample identities of the intensities of one peak (Fx4_CM10_high_C066628, in bold type). The clusters that contain the correct sample values are shown in the “Original Cluster” column at the indicated threshold CV, and after randomizing the sample intensities of just one peak on the right. The contributions (weights) of the components of the clusters are also shown.

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ISSN: 1756-0500

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