|
Data set comparison |
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| 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 |
|
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]. | |||||||
Lu et al. BMC Bioinformatics 2005 6:37 doi:10.1186/1471-2105-6-37 |
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