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Sample GSM1857 Query DataSets for GSM1857
Status Public on Jun 27, 2002
Title BC805B-AF
Sample type RNA
 
Channel 1
Source name CR1 reference
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name BC805B-AF
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Category: Primary tumor
Subcategory: Breast
Scanning Software: ScanAlyze
Software version: 2.44
Lot batch = svcc121
 
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
1 299 157 1985 2201 1935 337 266 396 2881 3277 .856 0 .537 .912 69 76 1.026 .689 .975 1.451 .785 1217 52 39 47 85 93 .537
2 325 162 1676 2209 1936 354 273 406 2882 3288 .784 0 .782 1.171 76 84 .866 .582 1.155 1.72 .847 1085 52 38 46 93 101 .782
3 359 168 1168 1372 1080 378 292 435 1608 2042 .727 0 .461 .91 76 69 1.081 .726 .925 1.377 .562 941 52 38 46 102 110 .461
4 361 168 705 869 571 390 298 444 850 1294 .63 0 .27 .781 65 61 1.235 .829 .81 1.206 .412 943 52 38 46 111 119 .27
5 304 162 2921 1687 1389 402 298 444 2068 2511 .836 0 -.498 .426 84 80 2.103 1.413 .476 .708 .43 945 52 38 46 120 128 -.498
6 284 156 2424 1932 1633 399 299 445 2431 2876 .853 0 .004 .717 88 94 1.484 .997 .674 1.003 .597 947 52 38 46 129 137 .004
7 289 160 1400 2005 1707 392 298 444 2541 2985 .828 0 .86 1.289 90 88 .82 .551 1.219 1.815 .964 943 52 38 46 138 146 .86
8 250 144 5418 3935 3630 387 305 454 5404 5858 .95 0 -.004 .613 78 63 1.493 1.003 .67 .997 .64 943 52 38 46 147 155 -.004
9 220 137 1318 1532 1227 372 305 454 1827 2281 .78 0 .471 .911 63 63 1.074 .722 .931 1.386 .739 963 52 37 45 156 164 .471
10 298 140 3974 3568 3252 433 316 470 4841 5312 .942 0 .285 .802 82 71 1.222 .821 .818 1.218 .768 963 52 37 45 165 173 .285
11 302 141 3458 3238 2916 450 322 479 4341 4820 .859 0 .328 .834 90 92 1.186 .797 .843 1.255 .761 955 52 37 45 174 182 .328
12 297 139 1709 1519 1193 456 326 485 1776 2261 .878 0 .055 .764 75 55 1.433 .962 .698 1.039 .671 947 52 37 45 183 191 .055
13 284 147 2265 2298 1967 452 331 493 2928 3421 .793 0 .371 .88 100 98 1.151 .774 .868 1.293 .69 939 52 37 45 191 199 .371
14 226 135 1033 1531 1199 389 332 494 1785 2279 .851 0 .789 1.13 75 69 .862 .579 1.161 1.728 .966 929 52 37 45 200 208 .789
15 204 134 14020 6398 6082 369 316 470 9054 9525 .921 0 -.631 .412 94 84 2.305 1.548 .434 .646 .423 931 52 37 45 209 217 -.631
16 207 135 1523 903 588 372 315 469 875 1344 .578 0 -.799 .382 84 71 2.59 1.74 .386 .575 .309 937 52 37 45 218 226 -.799
17 301 134 911 860 544 453 316 470 810 1280 .77 0 -.17 .669 84 57 1.675 1.125 .597 .889 .622 957 52 36 44 227 235 -.17
18 306 134 33 396 70 467 326 485 104 590 .731 0 1.659 2.326 30 28 .471 .317 2.121 3.158 .651 963 52 36 44 236 244 1.659
19 324 145 4714 5040 4700 481 340 506 6997 7503 .906 0 .57 1.041 88 90 1.003 .674 .997 1.484 .92 959 52 36 44 245 253 .57
20 438 137 1115 1011 648 534 363 540 965 1505 .752 0 -.209 .634 78 65 1.721 1.156 .581 .865 .424 955 52 36 44 254 262 -.209

Total number of rows: 9216

Table truncated, full table size 1129 Kbytes.




Supplementary data files not provided
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