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Sample GSM1847 Query DataSets for GSM1847
Status Public on Jun 27, 2002
Title BC709A-AF
Sample type RNA
 
Channel 1
Source name CR1 reference
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name BC709A-AF
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Category: Primary tumor
Subcategory: Breast
Scanning Software: ScanAlyze
Software version: 2.44
Lot batch = svcc85
 
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
1 268 207 2829 2496 2228 311 268 499 4151 4651 .904 0 .553 .732 69 67 1.27 .681 .788 1.467 .706 1229 52 44 52 87 95 .553
2 268 209 3828 1886 1625 302 261 486 3028 3514 .917 0 -.338 .441 78 71 2.356 1.264 .425 .791 .393 1057 52 45 53 96 104 -.338
3 268 205 2574 1811 1568 286 243 453 2922 3374 .875 0 .183 .676 75 69 1.642 .881 .609 1.135 .527 931 52 45 53 105 113 .183
4 264 202 1456 946 709 283 237 442 1321 1763 .821 0 -.14 .458 78 71 2.054 1.102 .487 .907 .416 931 52 45 53 113 121 -.14
5 263 201 4702 1417 1175 288 242 451 2189 2640 .814 0 -1.103 .272 73 84 4.002 2.148 .25 .466 .202 937 52 45 53 122 130 -1.103
6 256 194 2986 1624 1386 289 238 443 2582 3026 .917 0 -.209 .454 82 71 2.154 1.156 .464 .865 .429 943 52 45 53 131 139 -.209
7 260 204 1344 1638 1388 294 250 466 2586 3052 .848 0 .944 1.085 75 75 .968 .52 1.033 1.924 .902 943 52 45 53 140 148 .944
8 268 213 7264 1553 1296 301 257 479 2415 2894 .892 0 -1.589 .198 84 69 5.605 3.008 .178 .332 .161 943 52 45 53 149 157 -1.589
9 273 218 2559 1637 1385 293 252 470 2581 3050 .872 0 .012 .569 78 57 1.848 .992 .541 1.008 .476 943 52 45 53 158 166 .012
10 302 213 4698 2144 1893 304 251 468 3527 3995 .93 0 -.414 .416 67 55 2.482 1.332 .403 .751 .391 947 52 45 53 167 175 -.414
11 298 205 3275 1989 1735 306 254 473 3233 3706 .898 0 -.019 .473 73 67 1.888 1.013 .53 .987 .492 951 52 45 53 176 184 -.019
12 309 211 1885 741 491 300 250 466 915 1381 .799 0 -1.043 .317 69 57 3.839 2.06 .26 .485 .24 943 52 46 54 185 193 -1.043
13 305 208 3449 1833 1577 303 256 477 2938 3415 .869 0 -.231 .416 76 75 2.187 1.174 .457 .852 .402 947 52 46 54 194 202 -.231
14 279 205 1769 2364 2111 284 253 471 3933 4405 .868 0 1.153 1.136 84 80 .838 .45 1.193 2.223 1.067 951 52 46 54 203 211 1.153
15 289 216 16166 3331 3084 278 247 460 5746 6206 .944 0 -1.492 .19 75 63 5.242 2.813 .191 .355 .183 955 52 46 54 212 220 -1.492
16 280 207 1773 1005 759 283 246 458 1414 1873 .754 0 -.326 .47 80 80 2.336 1.254 .428 .798 .349 959 52 46 54 221 229 -.326
17 309 206 1039 1149 911 288 238 443 1697 2141 .821 0 .708 .815 67 59 1.141 .612 .877 1.634 .683 963 52 46 54 230 238 .708
18 305 202 77 333 89 291 244 455 166 620 .338 0 1.107 .541 32 26 .865 .464 1.156 2.154 .222 963 52 46 54 239 247 1.107
19 294 198 4721 2458 2212 291 246 458 4121 4580 .937 0 -.196 .492 75 67 2.134 1.145 .469 .873 .447 963 52 46 54 248 256 -.196
20 332 200 1921 1957 1707 294 250 466 3181 3646 .887 0 .727 .972 63 53 1.125 .604 .889 1.656 .807 963 52 46 54 257 265 .727

Total number of rows: 9216

Table truncated, full table size 1133 Kbytes.




Supplementary data files not provided
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