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Sample GSM1859 Query DataSets for GSM1859
Status Public on Jun 27, 2002
Title BC114B-AF
Sample type RNA
 
Channel 1
Source name CR1 reference
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name BC114B-AF
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Category: Primary tumor
Subcategory: Breast
Scanning Software: ScanAlyze
Software version: 2.44
Lot batch = svcc52
 
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 (3)
GSE61 Molecular portraits of human breast tumors
GSE4336 Breast tumors
GSE4382 Repeated observation of breast tumor subtypes in independent gene expression data sets

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
1 358 285 3095 4625 3201 1452 1424 1629 3662 5291 .952 0 .243 1.094 65 48 .967 .845 1.034 1.183 .972 1225 52 96 104 81 89 .243
2 378 306 2276 2995 1544 1466 1451 1660 1766 3426 .915 0 -.366 .684 75 51 1.474 1.289 .678 .776 .664 1069 52 96 104 90 98 -.366
3 390 314 2138 3060 1570 1504 1490 1705 1796 3501 .849 0 -.251 .664 73 44 1.362 1.19 .734 .84 .68 947 52 96 104 99 107 -.251
4 396 317 2020 2895 1377 1534 1518 1737 1575 3312 .801 0 -.359 .778 75 53 1.467 1.282 .682 .78 .541 951 52 96 104 108 116 -.359
5 397 320 5632 22069 20544 1533 1525 1745 23503 25248 .954 0 2.061 3.598 76 73 .274 .24 3.648 4.173 3.449 955 52 96 104 117 125 2.061
6 393 314 3188 4126 2623 1523 1503 1719 3001 4720 .863 0 -.087 .845 73 61 1.215 1.062 .823 .941 .784 959 52 96 104 126 134 -.087
7 377 307 541 2635 1160 1488 1475 1687 1327 3015 .645 0 1.295 2.2 63 50 .466 .408 2.144 2.453 1.262 951 52 96 104 135 143 1.295
8 362 294 8577 3544 2122 1428 1422 1627 2428 4054 .941 0 -1.821 .321 78 51 4.042 3.533 .247 .283 .227 931 52 97 105 144 152 -1.821
9 358 284 460 1821 430 1406 1391 1591 492 2083 .534 0 .097 .817 50 21 1.07 .935 .935 1.069 .571 921 52 97 105 152 160 .097
10 358 281 4677 5466 4079 1412 1387 1587 4667 6253 .932 0 -.003 .852 69 48 1.147 1.002 .872 .998 .826 921 52 97 105 161 169 -.003
11 358 267 2975 3041 1659 1411 1382 1581 1898 3479 .927 0 -.648 .569 78 55 1.793 1.567 .558 .638 .529 939 52 97 105 170 178 -.648
12 367 274 1230 1834 437 1419 1397 1598 500 2098 .751 0 -1.299 .484 65 34 2.815 2.46 .355 .406 .352 943 52 97 105 179 187 -1.299
13 365 269 689 1855 448 1428 1407 1610 513 2122 .615 0 -.427 .84 65 28 1.538 1.344 .65 .744 .444 947 52 97 105 187 195 -.427
14 369 279 933 3341 1918 1445 1423 1628 2194 3822 .804 0 1.234 2.298 67 48 .486 .425 2.056 2.352 1.679 957 52 97 105 196 204 1.234
15 370 289 9472 3105 1680 1438 1425 1630 1922 3552 .937 0 -2.301 .18 75 42 5.638 4.928 .177 .203 .18 963 52 97 105 205 213 -2.301
16 381 304 1453 1728 308 1436 1420 1625 352 1977 .403 0 -2.044 .233 71 19 4.718 4.124 .212 .243 .174 943 52 98 106 214 222 -2.044
17 379 307 1067 3549 2117 1441 1432 1638 2422 4060 .876 0 1.183 1.878 63 51 .504 .441 1.984 2.27 1.588 947 52 98 106 223 231 1.183
18 374 304 92 1415 1453 1444 1652 -33 1619 .251 0 .261 30 3 .229 951 52 98 106 232 240
19 371 302 4029 4769 3314 1464 1455 1665 3791 5456 .929 0 -.088 .899 73 61 1.216 1.063 .823 .941 .757 955 52 98 106 241 249 -.088
20 370 294 1030 3320 1872 1462 1448 1657 2142 3798 .818 0 1.056 1.545 61 48 .55 .481 1.817 2.079 1.451 955 52 98 106 250 258 1.056

Total number of rows: 9216

Table truncated, full table size 1152 Kbytes.




Supplementary data files not provided
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