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Sample GSM1896 Query DataSets for GSM1896
Status Public on Jun 27, 2002
Title BC710B-AF
Sample type RNA
 
Channel 1
Source name CR1 reference
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name BC710B-AF
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Category: Primary tumor
Subcategory: Breast
Scanning Software: ScanAlyze
Software version: 2.44
Lot batch = svcc82
 
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
1 345 270 3467 2810 2244 591 566 933 3698 4630 .945 0 .093 .692 75 55 1.545 .938 .647 1.066 .597 1213 52 49 57 112 120 .093
2 349 268 3193 2384 1824 592 560 923 3005 3928 .926 0 -.087 .604 65 57 1.751 1.062 .571 .941 .52 1069 52 49 57 120 128 -.087
3 332 255 2575 1926 1390 576 536 883 2290 3174 .916 0 -.169 .595 59 51 1.853 1.124 .54 .889 .506 925 52 49 57 129 137 -.169
4 330 254 2305 1006 486 558 520 857 801 1658 .776 0 -1.525 .225 75 50 4.743 2.878 .211 .347 .196 943 52 49 57 138 146 -1.525
5 336 276 7758 1844 1333 549 511 842 2196 3038 .874 0 -1.821 .189 73 59 5.82 3.532 .172 .283 .157 943 52 49 57 147 155 -1.821
6 454 312 2698 1886 1350 689 536 883 2224 3108 .819 0 -.278 .521 69 55 1.999 1.213 .5 .824 .423 947 52 49 57 156 164 -.278
7 620 369 1120 1349 758 917 591 974 1249 2223 .765 0 .157 .646 57 50 1.478 .897 .677 1.115 .624 951 52 49 57 165 173 .157
8 624 374 11962 3821 3217 928 604 995 5301 6296 .921 0 -1.174 .267 73 67 3.718 2.257 .269 .443 .246 955 52 49 57 174 182 -1.174
9 628 374 2842 3333 2726 936 607 1000 4492 5492 .777 0 .66 .849 84 80 1.043 .633 .959 1.58 .687 959 52 49 57 183 191 .66
10 625 364 6829 4413 3797 949 616 1015 6256 7271 .944 0 -.126 .546 73 55 1.799 1.092 .556 .916 .541 943 52 50 58 192 200 -.126
11 390 313 3924 2530 1967 622 563 928 3241 4169 .926 0 -.276 .529 61 55 1.995 1.211 .501 .826 .474 931 52 50 58 201 209 -.276
12 361 304 2418 1301 760 577 541 891 1252 2144 .874 0 -.949 .306 69 50 3.182 1.931 .314 .518 .303 931 52 50 58 210 218 -.949
13 371 319 909 953 404 593 549 905 666 1570 .702 0 -.449 .442 63 44 2.25 1.366 .444 .732 .415 925 52 50 58 218 226 -.449
14 367 304 1615 1387 838 600 549 905 1381 2285 .864 0 -.226 .576 71 53 1.927 1.17 .519 .855 .493 925 52 50 58 227 235 -.226
15 366 305 16242 3581 3045 588 536 883 5017 5901 .954 0 -1.695 .186 75 59 5.334 3.237 .187 .309 .175 947 52 50 58 236 244 -1.695
16 364 296 1818 899 372 590 527 868 613 1481 .644 0 -1.568 .179 59 40 4.887 2.966 .205 .337 .215 951 52 50 58 245 253 -1.568
17 358 292 1361 1606 1080 596 526 867 1780 2646 .787 0 .387 .716 71 55 1.26 .765 .794 1.308 .635 955 52 50 58 254 262 .387
18 370 293 496 619 532 877 -59 817 .194 0 .39 19 7 0 .296 959 52 50 58 263 271
19 385 306 6565 4381 3849 633 532 877 6342 7219 .951 0 -.05 .589 73 59 1.706 1.035 .586 .966 .586 943 52 51 59 272 280 -.05
20 402 307 1775 1237 701 647 536 883 1155 2038 .797 0 -.62 .402 73 55 2.532 1.537 .395 .651 .358 943 52 51 59 281 289 -.62

Total number of rows: 9216

Table truncated, full table size 1148 Kbytes.




Supplementary data files not provided
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