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Sample GSM1846 Query DataSets for GSM1846
Status Public on Jun 27, 2002
Title BC107B-BE
Sample type RNA
 
Channel 1
Source name CR1 reference
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name BC107B-BE
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Category: Primary tumor
Subcategory: Breast
Scanning Software: ScanAlyze
Software version: 2.44
Lot batch = svcc98
 
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 (6)
GSE61 Molecular portraits of human breast tumors
GSE3193 Breast Tumor Clinical Implications
GSE3281 Breast Cancer aCGH

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
1 640 531 4942 5433 3907 1688 1526 1962 5023 6985 .959 0 .024 .847 55 46 1.265 .984 .791 1.016 .776 1217 52 55 63 70 78 .024
2 632 530 5267 7881 6368 1653 1513 1945 8187 10133 .973 0 .636 1.216 67 50 .827 .643 1.209 1.554 1.215 1085 52 54 62 78 86 .636
3 621 532 5087 3729 2224 1602 1505 1935 2859 4794 .894 0 -.831 .477 65 51 2.287 1.779 .437 .562 .456 945 52 54 62 87 95 -.831
4 594 518 4111 1856 406 1545 1450 1864 522 2386 .308 0 -2.977 .087 63 25 10.126 7.876 .099 .127 .056 947 52 54 62 96 104 -2.977
5 610 520 18326 3025 1577 1553 1448 1862 2028 3889 .908 0 -3.176 .114 67 38 11.621 9.038 .086 .111 .085 949 52 54 62 105 113 -3.176
6 586 502 5610 5299 3875 1543 1424 1831 4982 6813 .948 0 -.171 .695 61 59 1.448 1.126 .691 .888 .633 951 52 54 62 114 122 -.171
7 564 471 1914 3767 2395 1501 1372 1764 3079 4843 .861 0 .686 1.414 63 61 .799 .622 1.251 1.609 .961 935 52 54 62 123 131 .686
8 550 458 17841 7251 5929 1480 1322 1700 7623 9323 .944 0 -1.227 .323 59 51 3.009 2.34 .332 .427 .315 931 52 54 62 132 140 -1.227
9 548 444 1676 2320 1036 1432 1284 1651 1332 2983 .9 0 -.331 .696 53 32 1.618 1.258 .618 .795 .615 925 52 54 62 140 148 -.331
10 563 435 8987 5858 4607 1452 1251 1608 5923 7532 .922 0 -.601 .609 51 48 1.951 1.517 .513 .659 .491 925 52 54 62 149 157 -.601
11 542 415 5992 4458 3258 1395 1200 1543 4189 5732 .934 0 -.516 .576 71 55 1.839 1.43 .544 .699 .533 943 52 54 62 158 166 -.516
12 499 420 3528 2796 1622 1325 1174 1509 2085 3595 .786 0 -.759 .479 65 53 2.175 1.692 .46 .591 .383 959 52 53 61 167 175 -.759
13 502 438 1610 2133 954 1316 1179 1516 1227 2742 .772 0 -.392 .647 69 51 1.688 1.313 .593 .762 .671 955 52 53 61 176 184 -.392
14 474 431 1876 3239 2070 1262 1169 1503 2661 4164 .871 0 .505 1.182 71 51 .906 .705 1.103 1.419 1.044 945 52 53 61 184 192 .505
15 464 414 14151 6789 5643 1232 1146 1473 7255 8729 .949 0 -.964 .433 73 57 2.508 1.95 .399 .513 .365 941 52 53 61 193 201 -.964
16 467 414 2750 1867 735 1215 1132 1455 945 2400 .722 0 -1.541 .302 57 48 3.741 2.91 .267 .344 .211 943 52 53 61 202 210 -1.541
17 475 411 1984 2073 949 1227 1124 1445 1220 2665 .829 0 -.701 .498 57 44 2.091 1.626 .478 .615 .471 945 52 53 61 211 219 -.701
18 462 398 58 1133 33 1204 1100 1414 42 1457 .523 0 -.451 .985 28 15 1.758 1.367 .569 .732 .863 947 52 53 61 220 228 -.451
19 483 414 8022 9341 8271 1208 1070 1376 10634 12010 .955 0 .407 1.041 82 76 .97 .754 1.031 1.326 .968 943 52 53 61 229 237 .407
20 479 411 1745 2462 1387 1217 1075 1382 1783 3165 .813 0 .031 .832 55 46 1.258 .979 .795 1.022 .683 943 52 53 61 238 246 .031

Total number of rows: 9216

Table truncated, full table size 1169 Kbytes.




Supplementary data files not provided
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