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Sample GSM98508 Query DataSets for GSM98508
Status Public on Mar 15, 2006
Title STT854-SS
Sample type RNA
 
Channel 1
Source name CRG mRNA
Organism Homo sapiens
Characteristics CRG mRNA
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name STT854 mRNA
Organism Homo sapiens
Characteristics STT854 mRNA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Primary tumor, Disease response
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16490.gif
Data processing VALUE is Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Feb 24, 2006
Last update date Sep 22, 2006
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 GPL2938
Series (2)
GSE4303 Gene expression profile of extraskeletal myxoid chondrosarcoma.
GSE4305 Determination of stromal signatures in breast carcinoma

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
VALUE 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
LOG_RAT2N_MEDIAN 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 VALUE LOG_RAT2N_MEDIAN
1 465 337 253 200 212 137 454 336 282 216 201 136 0 0 111 124 130 109 78 59 34 25 349 337 1.547 .646 .677 .749 .766 2.566 52 260 .784 .44 90 1660 9290 96 105 69 78 0 261 155 106 .501 261 105 1.995 .525 -.997 -.93
2 229 264 222 233 7 31 225 233 244 244 3 0 0 0 107 130 99 134 21 21 6 6 38 3 .226 4.429 null .922 .892 3.267 32 109 1.625 .33 60 1760 9290 98 104 81 87 0 205 181 24 3.435 181 0 .291 null 1.78 null
3 1564 1112 297 278 1267 834 1749 1233 594 468 1452 955 0 0 974 717 625 440 66 60 55 53 2101 2407 1.519 .658 .658 .779 .672 2.504 120 348 .692 .92 120 1920 9290 95 107 94 106 0 862 216 647 .511 956 741 1.959 .51 -.97 -.971
4 266 216 277 241 -11 -25 247 197 546 427 -30 -44 0 0 92 103 585 426 0 0 0 0 -36 -74 null null null 1.108 1.222 3.667 120 269 .669 .27 120 2050 9290 95 107 107 119 0 168 187 -19 null 153 -34 null null null null
5 692 616 300 255 392 361 714 591 421 363 414 336 0 0 273 296 272 274 64 64 30 23 753 750 1.086 .921 .812 .874 .958 2.198 120 274 1.032 .79 120 2190 9290 95 107 121 133 0 478 198 280 .714 458 261 1.4 .629 -.486 -.668
6 257 226 306 260 -49 -34 249 209 411 325 -57 -51 0 0 86 105 246 215 0 2 0 0 -83 -108 null null null 1.179 1.217 3.391 120 324 1.13 .18 120 2330 9290 95 107 135 147 0 175 202 -26 null 162 -40 null null null null
7 670 415 375 322 295 93 757 396 451 343 382 74 0 0 324 207 238 162 56 35 32 8 388 456 3.172 .315 .194 .477 .451 2.554 80 245 .432 .61 110 2500 9290 95 106 152 163 0 322 250 72 .244 307 57 4.09 .15 -2.032 -2.735
8 481 442 330 299 151 143 495 421 388 337 165 122 0 0 144 204 195 193 41 36 3 15 294 287 1.056 .947 .739 .94 1.116 3.685 120 282 1.179 .6 120 2610 9290 95 107 163 175 0 343 232 111 .734 327 95 1.362 .573 -.445 -.802
9 325 248 256 212 69 36 302 231 278 234 46 19 0 0 129 111 114 126 28 23 10 0 105 65 1.917 .522 .413 1.112 1.036 3.866 120 270 .543 .21 120 2740 9290 95 107 176 188 0 192 164 28 .405 179 15 2.471 .32 -1.305 -1.642
10 307 232 240 206 67 26 290 215 249 218 50 9 0 0 97 103 77 96 34 20 15 9 93 59 2.577 .388 .18 .753 .844 3.768 120 270 5.353 .05 120 2880 9290 95 107 190 202 0 180 160 20 .301 167 7 3.323 .14 -1.732 -2.841
11 875 268 230 216 645 52 906 248 240 225 676 32 0 0 428 114 73 95 85 31 82 11 697 708 12.404 .081 .047 .154 .146 3.353 120 283 .075 .29 120 3020 9280 94 106 204 216 0 208 168 40 .063 192 25 15.994 .037 -3.999 -4.768
12 336 271 238 215 98 56 292 239 247 225 54 24 0 0 185 134 77 105 42 32 31 13 154 78 1.75 .571 .444 .854 .924 3.844 120 271 .596 .36 120 3160 9280 94 106 218 230 0 210 167 43 .443 185 19 2.256 .345 -1.174 -1.537
13 376 336 239 213 137 123 368 311 248 224 129 98 0 0 158 156 78 111 56 48 45 27 260 227 1.114 .898 .76 .857 .959 3.086 120 269 1.121 .39 120 3290 9280 94 106 231 243 0 261 165 95 .696 241 76 1.436 .589 -.522 -.763
14 362 296 239 199 123 97 348 292 244 221 109 93 0 0 131 145 86 115 56 42 30 14 220 202 1.268 .789 .853 .939 .879 4.285 120 274 1.172 .24 120 3430 9280 94 106 245 257 0 230 154 75 .612 226 72 1.635 .662 -.709 -.596
15 288 242 234 204 54 38 289 206 241 220 55 2 0 0 106 133 87 108 31 23 15 10 92 57 1.421 .704 .036 1.109 1.049 4.312 120 274 5.055 .08 120 3570 9280 94 106 259 271 0 188 158 29 .546 160 2 1.832 .028 -.874 -5.148
16 634 419 224 214 410 205 685 402 232 224 461 188 0 0 262 188 79 107 85 60 78 47 615 649 2 .5 .408 .516 .55 2.479 120 271 .516 .63 120 3710 9280 94 106 273 285 0 325 166 159 .388 312 146 2.579 .316 -1.367 -1.661
17 321 346 206 207 115 139 305 320 207 214 99 113 0 0 116 175 78 107 56 52 29 31 254 212 .827 1.209 1.141 1.271 1.526 4.026 120 271 2.358 .35 120 3850 9280 94 106 287 299 0 268 161 108 .937 248 88 1.067 .885 -.093 -.176
18 394 300 185 201 209 99 398 261 225 238 213 60 0 0 121 146 209 164 50 33 3 7 308 273 2.111 .474 .282 .627 .698 3.861 120 263 1.358 .63 120 3980 9280 94 106 300 312 0 233 156 77 .367 202 47 2.722 .218 -1.445 -2.195
19 629 549 127 187 502 362 416 331 263 257 289 144 0 0 635 568 318 220 44 37 19 22 864 433 1.387 .721 .498 .652 .74 2.648 120 308 .804 .74 120 4120 9270 93 105 314 326 0 426 145 281 .559 257 112 1.788 .386 -.838 -1.372
20 110 184 92 167 18 17 82 178 240 243 -10 11 0 0 91 85 355 222 1 1 0 0 35 1 1.059 .944 null 1.882 1.555 5.134 80 205 1.12 .64 100 4220 9270 94 104 325 335 -50 143 130 13 .732 138 9 1.365 null -.449 null

Total number of rows: 44544

Table truncated, full table size 9769 Kbytes.




Supplementary data files not provided
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