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Table 1 Data set comparison

From: Can Zipf's law be adapted to normalize microarrays?

Set Microarray Platform Number of Data Points Number of Expts R2 GEO platform GEO experiment Array type
A. Human Unigene RZPD 1 34560 31 0.9877 GLP284 GSE1510 cDNA, membrane
B. Clontech Atlas Rat cDNA Expression 588 39 0.9968 GPL158 GSE1509 cDNA, membrane
C. Clontech Atlas Human 1.2 (I & II) 1176 10 0.9903 GPL127, GPL128 GSE751 cDNA, membrane
D. Clontech Atlas Mouse 1.2 1159 12 0.9460 GPL144 GSE565 cDNA, membrane
E. Clontech Atlas Human Cancer 1.2 1160 36 0.9109 GPL158 GSE796 cDNA, membrane
F. NlaIII: Rattus norvegicus 76790 1 0.9982 GPL23 GSM1679 SAGE
G. NlaIII: Homo sapiens 101677 1 0.9978 GPL4 GSM14771 SAGE
H. Mouse Apoptosis 1024 5 × 2 0.994 -- -- cDNA, glass
I. Caltech 16K cDNA mouse 908 58 0.8892 na na cDNA, glass
J. Stanford Human Unigene 908 24 0.9081 na na cDNA, glass
K. Affymetrix GeneChip Rat Genome 8799 24 0.8538 GPL85 GSE776 Oligo, glass
L. Affymetrix GeneChip Human Genome 12625 24 0.7773 GPL91 GSE803 Oligo, glass
  1. Eleven microarray data set comparison. Raw intensities, without background subtraction, were used. Controls and blanks were excluded. For Affymetrix chips (K and L), MM/PM ratios were used. For data set B two different Atlas arrays were analyzed together, when analyzed separately they gave similar results. For two channel array systems (I and J), each channel was treated as a separate array. For set I, only the cyanine-3 channel (spleen sample control) was used and for set J, both channels were used for analysis. Reference for data set J: Ross et. al. [31].