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Sample GSM1856 Query DataSets for GSM1856
Status Public on Jun 27, 2002
Title BC206B-AF
Sample type RNA
 
Channel 1
Source name CR1 reference
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name BC206B-AF
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Category: Primary tumor
Subcategory: Breast
Scanning Software: ScanAlyze
Software version: 2.44
Lot batch = svcc135
 
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 1002 632 6827 9105 7566 2224 1539 1788 8788 10575 .913 0 .364 1.134 67 67 .902 .777 1.108 1.287 1.025 1213 52 92 100 70 78 .364
2 980 622 4831 6939 5412 2241 1527 1774 6286 8060 .844 0 .38 1.12 71 75 .893 .769 1.12 1.301 .982 1085 52 91 99 78 86 .38
3 961 606 3652 5289 3825 2174 1464 1700 4443 6143 .772 0 .283 .875 65 55 .955 .822 1.047 1.217 .92 945 52 91 99 87 95 .283
4 948 593 3705 3363 1951 2061 1412 1640 2266 3906 .595 0 -.709 .461 71 61 1.899 1.635 .527 .612 .485 957 52 91 99 96 104 -.709
5 875 568 15759 5515 4194 1877 1321 1534 4871 6406 .818 0 -1.694 .313 75 69 3.758 3.235 .266 .309 .24 963 52 91 99 105 113 -1.694
6 819 559 7402 6127 4810 1919 1317 1530 5587 7117 .815 0 -.406 .66 88 86 1.539 1.325 .65 .755 .589 959 52 91 99 114 122 -.406
7 796 540 4615 4958 3645 1899 1313 1525 4234 5759 .764 0 -.124 .928 80 75 1.266 1.09 .79 .917 .68 943 52 91 99 123 131 -.124
8 771 536 20720 4772 3458 1918 1314 1526 4016 5543 .802 0 -2.367 .193 71 55 5.992 5.159 .167 .194 .155 939 52 91 99 132 140 -2.367
9 780 540 10067 7071 5761 1935 1310 1522 6691 8213 .854 0 -.589 .59 75 59 1.747 1.504 .572 .665 .483 929 52 91 99 140 148 -.589
10 794 539 13400 9234 7921 2013 1313 1525 9200 10725 .927 0 -.542 .59 67 65 1.692 1.456 .591 .687 .537 925 52 91 99 149 157 -.542
11 784 529 7927 6938 5643 1947 1295 1504 6554 8058 .841 0 -.274 .675 82 78 1.405 1.209 .712 .827 .663 943 52 91 99 158 166 -.274
12 799 523 4677 4417 3122 1992 1295 1504 3626 5130 .402 0 -.367 .432 67 55 1.498 1.29 .668 .775 .398 939 52 91 99 167 175 -.367
13 764 507 4427 4297 2987 1975 1310 1522 3469 4991 .716 0 -.352 .67 88 78 1.482 1.276 .675 .784 .644 935 52 91 99 176 184 -.352
14 798 547 2649 3669 2243 2156 1426 1656 2605 4262 .765 0 -.024 .806 71 57 1.181 1.017 .847 .983 1.016 925 52 91 99 184 192 -.024
15 792 564 24035 7806 6268 2263 1538 1786 7280 9067 .859 0 -1.723 .265 84 65 3.835 3.301 .261 .303 .22 925 52 91 99 193 201 -1.723
16 906 595 4056 3552 1896 2481 1656 1923 2202 4126 .292 0 -.881 .307 86 55 2.139 1.842 .467 .543 .392 951 52 90 98 202 210 -.881
17 976 632 2429 3449 1753 2582 1696 1970 2036 4006 .625 0 -.255 .764 75 65 1.386 1.193 .722 .838 .758 957 52 90 98 211 219 -.255
18 986 632 64 1333 2634 1665 1934 -386 1548 .664 0 1.594 17 3 1.204 963 52 90 98 220 228
19 932 598 10527 10876 9269 2490 1607 1867 10766 12632 .89 0 .032 .899 90 86 1.136 .978 .88 1.023 .793 963 52 90 98 229 237 .032
20 824 564 3050 4409 2851 2230 1558 1810 3311 5121 .691 0 .119 .845 63 59 1.07 .921 .935 1.086 .927 963 52 90 98 238 246 .119

Total number of rows: 9216

Table truncated, full table size 1192 Kbytes.




Supplementary data files not provided
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