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Sample GSM1849 Query DataSets for GSM1849
Status Public on Jun 27, 2002
Title BC1369
Sample type RNA
 
Channel 1
Source name CR1 reference
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name BC1369
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Category: Primary tumor
Subcategory: Breast
Scanning Software: ScanAlyze
Software version: 2.44
Lot batch = svcc132
 
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 (5)
GSE61 Molecular portraits of human breast tumors
GSE3193 Breast Tumor Clinical Implications
GSE4268 Breast and ovarian carcinoma

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
1 887 635 3141 7951 6684 1434 1267 1426 7524 8950 .88 0 1.26 2.097 59 57 .47 .417 2.128 2.395 1.698 1213 52 87 95 92 100 1.26
2 893 607 3952 5833 4590 1415 1243 1399 5167 6566 .857 0 .387 1.18 71 61 .861 .765 1.161 1.307 .965 1069 52 87 95 100 108 .387
3 937 608 2502 2565 1318 1488 1247 1404 1484 2887 .698 0 -.754 .614 69 55 1.898 1.686 .527 .593 .53 937 52 87 95 109 117 -.754
4 869 610 2313 1830 588 1461 1242 1398 662 2060 .566 0 -1.805 .278 73 38 3.934 3.495 .254 .286 .395 943 52 87 95 118 126 -1.805
5 767 617 7728 4143 2921 1390 1222 1375 3288 4663 .848 0 -1.233 .367 71 71 2.646 2.35 .378 .425 .347 943 52 87 95 127 135 -1.233
6 749 606 4863 3021 1763 1415 1258 1416 1984 3400 .686 0 -1.293 .354 86 78 2.758 2.451 .363 .408 .397 943 52 87 95 136 144 -1.293
7 747 592 1382 3384 2171 1384 1213 1365 2444 3809 .789 0 .822 1.345 71 78 .637 .566 1.571 1.768 1.1 943 52 87 95 145 153 .822
8 678 566 12577 10948 9737 1327 1211 1363 10960 12323 .961 0 -.199 .822 71 75 1.292 1.148 .774 .871 .748 943 52 87 95 154 162 -.199
9 811 575 1805 3233 2033 1558 1200 1351 2288 3639 .726 0 .342 .988 75 53 .888 .789 1.126 1.268 1.13 943 52 87 95 163 171 .342
10 963 619 6975 6352 5136 1889 1216 1369 5781 7150 .797 0 -.271 .724 73 55 1.358 1.207 .736 .829 .726 939 52 87 95 172 180 -.271
11 983 632 5183 11448 10200 1924 1248 1405 11481 12886 .874 0 1.147 2.091 96 88 .508 .451 1.968 2.215 1.75 931 52 87 95 181 189 1.147
12 983 633 2383 3610 2370 1946 1240 1396 2668 4063 .79 0 .163 1.15 63 50 1.005 .893 .995 1.119 1.242 931 52 87 95 190 198 .163
13 915 620 2138 3316 2077 1846 1239 1395 2338 3733 .787 0 .129 .965 76 67 1.029 .914 .971 1.093 1.312 925 52 87 95 198 206 .129
14 748 614 1416 2386 1135 1440 1251 1408 1278 2686 .591 0 -.148 1.165 57 51 1.248 1.108 .802 .902 .731 931 52 87 95 207 215 -.148
15 720 613 20882 11245 10020 1359 1225 1379 11279 12658 .914 0 -.889 .457 69 73 2.084 1.851 .48 .54 .438 943 52 87 95 216 224 -.889
16 727 604 2704 1755 536 1335 1219 1372 603 1975 .417 0 -2.164 .189 82 44 5.045 4.482 .198 .223 .215 943 52 87 95 225 233 -2.164
17 794 610 1662 2006 776 1349 1230 1385 873 2258 .437 0 -.928 .487 71 48 2.142 1.903 .467 .526 .318 943 52 87 95 234 242 -.928
18 789 582 151 1337 107 1405 1230 1385 120 1505 .249 0 -.326 1.24 38 25 1.411 1.254 .709 .798 .383 947 52 87 95 243 251 -.326
19 801 604 6773 15789 14603 1361 1186 1335 16437 17772 .889 0 1.279 2.015 94 90 .464 .412 2.156 2.427 1.849 951 52 87 95 252 260 1.279
20 817 616 1966 2918 1729 1355 1189 1338 1946 3285 .732 0 -.015 .967 71 55 1.137 1.01 .879 .99 .746 955 52 87 95 261 269 -.015

Total number of rows: 9216

Table truncated, full table size 1162 Kbytes.




Supplementary data files not provided
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