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Sample GSM1883 Query DataSets for GSM1883
Status Public on Jun 27, 2002
Title MDA-MB-231-NCI
Sample type RNA
 
Channel 1
Source name CR1 reference
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name MDA-MB-231
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Category: Cell-line
Subcategory: Breast
MDA-MB-231 isolate obtained from NCI60 cell line set
Scanning Software: ScanAlyze
Software version: 2.44
Lot batch = svcc73
 
Submission date Jun 18, 2002
Last update date Nov 21, 2005
Organization Stanford Microarray Database (SMD)
E-mail(s) [email protected]
Phone 650-498-6012
URL http://genome-www5.stanford.edu/
Department Stanford University, School of Medicine
Street address 300 Pasteur Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL180
Series (1)
GSE61 Molecular portraits of human breast tumors

Data table header descriptions
ID_REF
CH1B_MEAN mean channel 1 background
CH1B_MEDIAN median channel 1 background
CH1D_MEAN difference between CH1I_MEAN and CH1B_MEAN
CH2I_MEAN mean channel 2 signal
CH2D_MEAN difference of CH2I_MEAN and CH2B_MEAN
CH2B_MEAN mean of channel 2 background
CH2B_MEDIAN median of channel 2 background
CH2BN_MEDIAN normalized CH2B_MEDIAN
CH2DN_MEAN normalized CH2D_MEAN
CH2IN_MEAN normalized CH2I_MEAN
CORR simple correlation coefficient of channel 1 and channel 2 pixels
FLAG user defined flag (default=0)
VALUE same as UNF_VALUE but with flagged values removed
PIX_RAT2_MEDIAN
PERGTBCH1I_1SD standard deviation of fraction of pixels greater than CH1B_MEAN
PERGTBCH2I_1SD standard deviation of fraction of pixels greater than CH2B_MEAN
RAT1_MEAN ratio of CH1D_MEAN to CH2D_MEAN
RAT1N_MEAN ratio of CH1DN_MEAN to CH2DN_MEAN
RAT2_MEAN ratio of CH2D_MEAN to CH1D_MEAN
RAT2N_MEAN ratio of CH2DN_MEAN and CH1DN_MEAN
REGR slope of the simple regression line of channel 2 to channel 1 pixels
TOT_BPIX total number of background pixels
TOT_SPIX total number of signal (spot) pixels
TOP vertical, short-axis spot ellipse minimum pixel coordinate
BOT vertical, short-axis spot ellipse maximum pixel coordinate
LEFT horizontal, long-axis spot ellipse minimum pixel coordinate
RIGHT horizontal, long-axis spot ellipse maximum pixel coordinate
UNF_VALUE aka LOG_RAT2N_MEAN, or log10 of ratio of CH2DN_MEAN and CH1DN_MEAN

Data table
ID_REF CH1B_MEAN CH1B_MEDIAN CH1D_MEAN CH2I_MEAN CH2D_MEAN CH2B_MEAN CH2B_MEDIAN CH2BN_MEDIAN CH2DN_MEAN CH2IN_MEAN CORR FLAG VALUE PIX_RAT2_MEDIAN PERGTBCH1I_1SD PERGTBCH2I_1SD RAT1_MEAN RAT1N_MEAN RAT2_MEAN RAT2N_MEAN REGR TOT_BPIX TOT_SPIX TOP BOT LEFT RIGHT UNF_VALUE
1 584 447 1411 2847 1772 1162 1075 1053 1738 2791 .889 0 .301 .909 61 46 .796 .812 1.256 1.232 1.139 1294 52 28 36 71 79 .301
2 581 430 1511 2270 1268 1099 1002 982 1243 2225 .785 0 -.282 .815 84 84 1.192 1.216 .839 .823 .817 1144 52 28 36 80 88 -.282
3 690 422 1141 2036 1126 1247 910 892 1104 1996 .835 0 -.048 .833 76 71 1.013 1.034 .987 .968 1.197 981 52 29 37 89 97 -.048
4 711 422 848 833 1190 868 850 816 .638 0 .144 76 0 .828 986 52 29 37 97 105
5 830 457 1805 952 104 1305 848 831 102 933 .484 0 -4.145 .104 90 5 17.356 17.696 .058 .057 .452 986 52 29 37 106 114 -4.145
6 937 463 1135 1673 814 1426 859 842 798 1640 .834 0 -.508 .754 71 55 1.394 1.422 .717 .703 .984 992 52 29 37 115 123 -.508
7 946 477 1760 2633 1751 1449 882 864 1717 2581 .878 0 -.036 .986 80 75 1.005 1.025 .995 .976 1.017 973 52 29 37 124 132 -.036
8 827 457 3470 5469 4591 1263 878 860 4501 5361 .939 0 .375 1.249 84 73 .756 .771 1.323 1.297 1.254 973 52 29 37 133 141 .375
9 623 394 318 1295 453 1071 842 825 444 1269 .814 0 .482 1.764 40 36 .702 .716 1.425 1.396 .945 959 52 29 37 141 149 .482
10 602 376 2299 4376 3565 1035 811 795 3495 4290 .901 0 .604 1.409 69 53 .645 .658 1.551 1.52 1.357 959 52 29 37 150 158 .604
11 523 368 1709 4070 3291 937 779 763 3227 3990 .87 0 .917 1.737 80 69 .519 .53 1.926 1.888 1.642 965 52 29 37 159 167 .917
12 536 370 777 1690 927 924 763 748 908 1656 .814 0 .225 1.009 61 46 .838 .856 1.193 1.169 .907 999 52 29 37 168 176 .225
13 652 379 636 1252 502 1093 750 735 492 1227 .861 0 -.37 .704 71 44 1.267 1.293 .789 .774 1.27 1021 52 29 37 177 185 -.37
14 620 387 533 968 228 1016 740 725 224 949 .876 0 -1.251 .316 69 25 2.338 2.379 .428 .42 1.36 985 52 30 38 189 197 -1.251
15 600 387 4163 11769 11030 999 739 724 10814 11538 .957 0 1.377 2.415 57 57 .377 .385 2.65 2.598 2.347 998 52 29 37 199 207 1.377
16 607 387 636 1083 353 1024 730 715 346 1061 .851 0 -.878 .564 61 38 1.802 1.838 .555 .544 1.255 970 52 29 37 208 216 -.878
17 558 399 428 2010 1268 941 742 727 1243 1970 .728 0 1.538 3.022 57 53 .338 .344 2.963 2.904 1.392 943 52 29 37 217 225 1.538
18 673 396 250 1038 274 1024 764 749 268 1017 .803 0 .1 .723 34 13 .912 .933 1.096 1.072 .532 943 52 29 37 226 234 .1
19 718 410 1700 3484 2698 1158 786 770 2645 3415 .789 0 .638 1.439 73 61 .63 .643 1.587 1.556 .936 939 52 29 37 235 243 .638
20 755 405 531 1180 368 1180 812 796 360 1156 .709 0 -.561 .466 59 30 1.443 1.475 .693 .678 .684 931 52 29 37 244 252 -.561

Total number of rows: 9216

Table truncated, full table size 1132 Kbytes.




Supplementary data files not provided
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