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Sample GSM90603 Query DataSets for GSM90603
Status Public on Jan 06, 2006
Title ULL-D-202
Sample type RNA
 
Channel 1
Source name Stratagene_aT
Organism Homo sapiens
Characteristics reference: Stratagene Reference, amplified total RNA
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name ULL-D-202_aT
Organism Homo sapiens
Characteristics cell type: primary breast carcinoma
ID: ULL-D-202
Extracted molecule total RNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol not provided
Description Simple annotation: Breast, primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24819.gif
Scanner Make: Axon
name: 24819_Scanner Make
Data processing VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Jan 04, 2006
Last update date Sep 18, 2012
Organization Stanford Microarray Database (SMD)
E-mail(s) array@genome.stanford.edu
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 GPL2790
Series (2)
GSE3971 Invasive lobular and ductal carcinomas of the breast
GSE40954 TP53 mutation status and gene expression profiles are powerful prognostic markers of breast cancer

Data table header descriptions
ID_REF ID_REF
CH1I_MEAN Mean feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEAN Mean feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEDIAN The median feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_MEDIAN The median feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH1D_MEAN The mean feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2D_MEAN .The mean feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1I_MEDIAN Median feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEDIAN Median feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEAN The mean feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Background
CH2B_MEAN The mean feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Background
CH1D_MEDIAN The median feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH2D_MEDIAN The median feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH1_PER_SAT The percentage of feature pixels at wavelength 532 nm that are saturated.; Type: integer; Scale: linear_scale
CH2_PER_SAT The percentage of feature pixels at wavelength 635 nm that are saturated.; Type: integer; Scale: linear_scale
CH1I_SD The standard deviation of the feature intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2I_SD The standard deviation of the feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1B_SD The standard deviation of the feature background intensity at wavelength 532 nm.; Type: float; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_SD The standard deviation of the feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
PERGTBCH1I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 635 nm.; Type: integer; Scale: linear_scale
PERGTBCH1I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
SUM_MEAN The sum of the arithmetic mean intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
SUM_MEDIAN The sum of the median intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
RAT1_MEAN Ratio of the arithmetic mean intensities of each spot for each wavelength, with the median background subtracted. Channel 1/Channel 2 ratio, (CH1I_MEAN - CH1B_MEDIAN)/(CH2I_MEAN - CH2B_MEDIAN) or Green/Red ratio.; Type: float; Scale: linear_scale
RAT2_MEAN The ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_MEDIAN The ratio of the median intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEAN The geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEDIAN The median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_SD The geometric standard deviation of the pixel intensity ratios.; Type: float; Scale: linear_scale
TOT_SPIX The total number of feature pixels.; Type: integer; Scale: linear_scale
TOT_BPIX The total number of background pixels.; Type: integer; Scale: linear_scale
REGR The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature.; Type: float; Scale: linear_scale
CORR The correlation between channel1 (Cy3) & Channel 2 (Cy5) pixels within the spot, and is a useful quality control parameter. Generally, high values imply better fit & good spot quality.; Type: float; Scale: linear_scale
DIAMETER The diameter in um of the feature-indicator.; Type: integer; Scale: linear_scale
X_COORD X-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
Y_COORD Y-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
TOP Box top: int(((centerX - radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
BOT Box bottom: int(((centerX + radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
LEFT Box left: int(((centerY - radius) - yoffset) / pixelSize).; Type: integer; Scale: linear_scale
RIGHT Box right: int(((centerY + radius) - yoffset) / pixelSize); Type: integer; Scale: linear_scale
FLAG The type of flag associated with a feature: -100 = user-flagged null spot; -50 = software-flagged null spot; 0 = spot valid.; Type: integer; Scale: linear_scale
CH2IN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
RAT2N_MEAN Type: float; Scale: linear_scale
CH2IN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEDIAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale
RAT1N_MEAN Ratio of the means of Channel 1 (usually 532 nm) intensity to normalized Channel 2 (usually 635 nm) intensity with median background subtracted (CH1D_MEAN/CH2DN_MEAN). Channel 1/Channel 2 ratio normalized or Green/Red ratio normalized.; Type: float; Scale: linear_scale
RAT2N_MEDIAN Channel 2/Channel 1 ratio normalized, RAT2_MEDIAN/Normalization factor or Red/Green median ratio normalized.; Type: float; Scale: linear_scale
LOG_RAT2N_MEAN Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEAN)].; Type: float; Scale: log_base_2
VALUE Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEDIAN)].; Type: float; Scale: log_base_2

Data table
ID_REF CH1I_MEAN CH2I_MEAN CH1B_MEDIAN CH2B_MEDIAN CH1D_MEAN CH2D_MEAN CH1I_MEDIAN CH2I_MEDIAN CH1B_MEAN CH2B_MEAN CH1D_MEDIAN CH2D_MEDIAN CH1_PER_SAT CH2_PER_SAT CH1I_SD CH2I_SD CH1B_SD CH2B_SD PERGTBCH1I_1SD PERGTBCH2I_1SD PERGTBCH1I_2SD PERGTBCH2I_2SD SUM_MEAN SUM_MEDIAN RAT1_MEAN RAT2_MEAN RAT2_MEDIAN PIX_RAT2_MEAN PIX_RAT2_MEDIAN RAT2_SD TOT_SPIX TOT_BPIX REGR CORR DIAMETER X_COORD Y_COORD TOP BOT LEFT RIGHT FLAG CH2IN_MEAN CH2BN_MEDIAN CH2DN_MEAN RAT2N_MEAN CH2IN_MEDIAN CH2DN_MEDIAN RAT1N_MEAN RAT2N_MEDIAN LOG_RAT2N_MEAN VALUE
1 2104 1449 207 266 1897 1183 2249 1486 169 208 2042 1220 0 0 580 330 124 148 100 100 96 98 3080 3262 1.604 .624 .597 .64 .647 1.261 52 270 .621 .96 80 1790 8090 69 77 59 67 0 1509 277 1232 .65 1548 1271 1.539 .622 -.622 -.684
2 2123 1292 48 50 2075 1242 2317 1350 51 53 2269 1300 0 0 726 363 23 19 100 100 100 100 3317 3569 1.671 .599 .573 .625 .598 1.284 80 321 .572 .98 100 1940 8100 69 79 73 83 0 1346 52 1294 .623 1406 1354 1.604 .597 -.682 -.745
3 5045 15383 57 61 4988 15322 5258 15405 124 161 5201 15344 0 0 1746 6172 123 203 100 100 100 100 20310 20545 .326 3.072 2.95 3.028 3.114 1.286 80 400 3.17 .97 110 2070 8100 68 79 85 96 0 16024 64 15960 3.2 16047 15983 .313 3.073 1.678 1.62
4 23881 16669 269 355 23612 16314 28209 18537 288 340 27940 18182 0 0 11053 7725 378 274 100 100 100 100 39926 46122 1.447 .691 .651 .719 .7 1.406 52 348 .682 .98 90 2220 8090 68 77 101 110 0 17364 370 16994 .72 19309 18940 1.389 .678 -.475 -.561
5 4769 3233 345 449 4424 2784 4671 3146 458 500 4326 2697 0 0 476 407 427 331 100 100 100 100 7208 7023 1.589 .629 .623 .627 .605 1.085 12 104 .632 .97 50 2370 8090 70 75 118 123 0 3368 468 2900 .656 3277 2809 1.526 .649 -.609 -.623
6 1325 1510 310 422 1015 1088 1394 1644 334 428 1084 1222 0 0 400 380 190 146 94 98 86 94 2103 2306 .933 1.072 1.127 1.136 1.091 1.58 52 351 1.033 .95 90 2530 8090 68 77 132 141 0 1573 440 1133 1.117 1713 1273 .896 1.174 .159 .232
7 1594 2045 303 411 1291 1634 1620 2068 301 407 1317 1657 0 0 330 406 57 70 100 100 100 100 2925 2974 .79 1.266 1.258 1.269 1.288 1.197 52 288 1.274 .97 90 2660 8090 68 77 145 154 0 2130 428 1702 1.318 2154 1726 .758 1.311 .399 .39
8 15055 11761 295 401 14760 11360 16155 12871 304 411 15860 12470 0 0 4297 3329 76 76 100 100 100 100 26120 28330 1.299 .77 .786 .77 .784 1.211 52 325 .762 .98 90 2800 8090 68 77 159 168 0 12251 418 11833 .802 13407 12990 1.247 .819 -.319 -.288
9 5218 9652 280 375 4938 9277 5544 9996 284 394 5264 9621 0 0 1409 2822 45 147 100 100 100 100 14215 14885 .532 1.879 1.828 1.877 1.918 1.209 52 313 1.873 .97 90 2950 8090 68 77 174 183 0 10054 391 9664 1.957 10413 10022 .511 1.904 .969 .929
10 1922 8198 263 350 1659 7848 2007 8441 269 353 1744 8091 0 0 707 3335 42 58 100 100 100 100 9507 9835 .211 4.731 4.639 4.761 4.798 1.265 52 289 4.816 .98 90 3100 8090 68 77 189 198 0 8540 365 8175 4.928 8793 8428 .203 4.833 2.301 2.273
11 11574 9749 265 347 11309 9402 12151 10619 277 370 11886 10272 0 0 2776 2587 95 182 100 100 100 100 20711 22158 1.203 .831 .864 .822 .842 1.186 80 400 .824 .98 110 3240 8090 67 78 202 213 0 10155 361 9794 .866 11061 10700 1.155 .9 -.208 -.152
12 5700 2705 267 352 5433 2353 5763 2624 297 391 5496 2272 0 0 1788 885 160 221 100 100 100 100 7786 7768 2.309 .433 .413 .424 .434 1.361 52 315 .422 .97 90 3390 8080 67 76 218 227 0 2818 367 2451 .451 2733 2367 2.217 .431 -1.148 -1.216
13 5194 5065 256 345 4938 4720 5300 5230 322 429 5044 4885 0 0 1124 1041 392 444 100 100 100 100 9658 9929 1.046 .956 .968 .96 .951 1.211 52 293 .941 .98 90 3540 8080 67 76 233 242 0 5276 359 4917 .996 5448 5089 1.004 1.009 -.006 .013
14 1150 817 248 329 902 488 1190 856 274 364 942 527 0 0 376 232 251 307 92 78 83 30 1390 1469 1.848 .541 .559 .521 .572 1.382 80 348 .546 .94 100 3690 8090 68 78 248 258 0 851 343 508 .564 892 549 1.774 .583 -.827 -.779
15 9266 8002 247 329 9019 7673 10306 8605 249 333 10059 8276 0 0 3530 2742 35 48 98 100 97 100 16692 18335 1.175 .851 .823 .935 .833 1.673 80 347 .825 .98 100 3840 8090 68 78 263 273 0 8335 343 7993 .886 8964 8621 1.128 .857 -.174 -.223
16 8660 7732 241 326 8419 7406 9533 8157 242 328 9292 7831 0 0 3105 2549 34 48 100 100 100 100 15825 17123 1.137 .88 .843 .91 .874 1.247 80 330 .844 .98 100 3980 8100 69 79 277 287 0 8054 340 7715 .916 8497 8157 1.091 .878 -.126 -.188
17 1316 1519 241 334 1075 1185 1321 1543 244 332 1080 1209 0 0 293 309 37 51 100 100 100 100 2260 2289 .907 1.102 1.119 1.105 1.115 1.33 52 289 1.104 .95 90 4130 8090 68 77 292 301 0 1582 348 1234 1.148 1607 1259 .871 1.166 .199 .222
18 750 761 255 341 495 420 755 768 257 344 500 427 0 0 135 148 40 56 100 100 100 100 915 927 1.179 .848 .854 .819 .818 1.353 52 271 .845 .92 90 4270 8090 68 77 306 315 0 793 355 438 .884 800 445 1.131 .89 -.178 -.169
19 3494 3790 261 348 3233 3442 3802 4100 266 353 3541 3752 0 0 1376 1225 45 63 99 100 95 99 6675 7293 .939 1.065 1.06 1.225 1.059 1.719 120 426 1.027 .98 120 4420 8100 68 80 320 332 0 3948 363 3585 1.109 4271 3908 .902 1.104 .149 .142
20 1355 2598 264 351 1091 2247 1438 2789 269 358 1174 2438 0 0 332 620 45 66 100 100 100 100 3338 3612 .486 2.06 2.077 2.085 2.164 1.308 52 258 2.051 .97 90 4560 8090 68 77 335 344 0 2706 366 2341 2.145 2905 2540 .466 2.163 1.101 1.113

Total number of rows: 43008

Table truncated, full table size 9810 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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