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Sample GSM39890 Query DataSets for GSM39890
Status Public on Feb 21, 2005
Title Colon, ascending 0222
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Colon, ascending 0222
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-10/20950.gif
 
Submission date Jan 26, 2005
Last update date Nov 22, 2005
Contact name Jonathan Pollack
E-mail(s) pollack1@stanford.edu
Phone 650-736-1987
Organization name Stanford University
Department Pathology
Lab Pollack Lab
Street address 269 Campus Drive, CCSR3245A
City Stanford
State/province CA
ZIP/Postal code 94305-5176
Country USA
 
Platform ID GPL1823
Series (1)
GSE2193 Normal_human_tissues

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 same as UNF_VALUE but with flagged values removed
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
UNF_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

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 UNF_VALUE
1 464 488 156 157 308 331 478 510 161 163 322 353 0 0 149 189 41 49 93 90 90 84 639 675 .931 1.075 1.096 .962 1.008 1.875 32 212 1.115 .85 70 1420 7280 28 35 62 69 0 397 128 269 .874 415 287 1.145 .891 -.195 -.166 -.195
2 312 402 158 160 154 242 312 415 162 162 154 255 0 0 98 141 42 45 88 88 82 82 396 409 .636 1.571 1.656 1.557 1.392 1.874 52 269 1.75 .74 80 1560 7270 27 35 76 84 0 327 130 197 1.278 337 207 .783 1.346 .353 .429 .353
3 1068 945 166 160 902 785 1118 1018 170 166 952 858 0 0 446 385 41 45 96 100 94 96 1687 1810 1.149 .87 .901 .837 .825 1.566 52 276 .849 .93 80 1710 7270 27 35 91 99 0 768 130 638 .708 828 698 1.413 .733 -.499 -.449 -.499
4 2773 7590 172 170 2601 7420 2618 6647 174 175 2446 6477 0 0 1429 4215 41 46 100 100 100 100 10021 8923 .351 2.853 2.648 2.931 2.741 1.543 52 280 2.974 .96 80 1860 7270 27 35 106 114 0 6171 138 6033 2.319 5404 5266 .431 2.153 1.214 1.106 1.214
5 453 799 172 169 281 630 524 866 180 174 352 697 0 0 185 354 42 48 84 87 84 84 911 1049 .446 2.242 1.98 1.997 2.063 1.687 32 171 2.399 .9 60 2000 7280 29 35 121 127 0 650 137 512 1.823 704 567 .549 1.61 .866 .687 .866
6 326 467 167 167 159 300 344 472 169 172 177 305 0 0 134 162 38 43 81 93 71 87 459 482 .53 1.887 1.723 1.738 1.669 2.075 32 164 1.744 .78 60 2140 7280 29 35 135 141 0 380 136 244 1.534 384 248 .652 1.401 .617 .486 .617
7 604 853 168 181 436 672 618 882 172 183 450 701 0 0 198 254 40 46 92 98 90 94 1108 1151 .649 1.541 1.558 1.444 1.441 1.574 52 256 1.49 .91 80 2290 7270 27 35 149 157 0 693 147 546 1.253 717 570 .798 1.266 .325 .341 .325
8 4384 7675 176 171 4208 7504 4660 7771 178 175 4484 7600 0 0 1953 3122 42 47 100 100 100 100 11712 12084 .561 1.783 1.695 2.007 1.762 1.764 52 301 1.779 .97 90 2440 7270 26 35 163 172 0 6240 139 6101 1.45 6318 6179 .69 1.378 .536 .463 .536
9 670 1676 176 167 494 1509 731 1732 177 172 555 1565 0 0 285 649 39 46 94 100 90 100 2003 2120 .327 3.055 2.82 3.523 3.012 1.86 52 269 2.96 .93 80 2580 7270 27 35 178 186 0 1363 136 1227 2.483 1408 1272 .403 2.293 1.312 1.197 1.312
10 401 588 176 164 225 424 396 572 176 172 220 408 0 0 118 188 39 46 93 100 90 100 649 628 .531 1.884 1.855 1.814 1.605 1.506 32 212 1.903 .83 70 2730 7270 27 34 193 200 0 478 133 345 1.532 465 332 .653 1.508 .615 .592 .615
11 823 985 169 169 654 816 868 883 170 172 699 714 0 0 445 493 40 48 96 100 94 96 1470 1413 .801 1.248 1.021 1.413 1.323 1.754 52 257 1.207 .94 80 2870 7280 28 36 207 215 0 801 137 663 1.014 718 580 .986 .83 .021 -.268 .021
12 855 1094 167 173 688 921 893 1131 178 192 726 958 0 0 277 305 111 232 94 98 92 88 1609 1684 .747 1.339 1.32 1.374 1.291 1.456 52 266 1.3 .94 80 3010 7270 27 35 221 229 0 889 141 749 1.088 920 779 .919 1.073 .122 .101 .122
13 668 1098 173 174 495 924 703 1127 185 200 530 953 0 0 203 305 118 252 93 96 90 87 1419 1483 .536 1.867 1.798 1.909 2.065 1.474 32 224 2.026 .88 70 3160 7270 27 34 236 243 0 893 141 751 1.518 916 775 .659 1.462 .602 .548 .602
14 418 543 174 176 244 367 434 525 175 179 260 349 0 0 136 179 40 50 90 96 90 90 611 609 .665 1.504 1.342 1.364 1.421 1.598 32 218 1.658 .8 70 3310 7270 27 34 251 258 0 441 143 298 1.223 427 284 .818 1.091 .29 .126 .29
15 2325 2914 168 182 2157 2732 2716 3055 168 184 2548 2873 0 0 1291 1679 42 46 97 98 95 97 4889 5421 .79 1.267 1.128 1.271 1.262 1.789 80 390 1.282 .98 100 3460 7270 26 36 265 275 0 2369 148 2221 1.03 2484 2336 .971 .917 .042 -.125 .042
16 989 2652 164 186 825 2466 1165 2998 165 190 1001 2812 0 0 445 1327 39 52 91 97 90 93 3291 3813 .335 2.989 2.809 2.819 3.091 1.666 80 382 3.065 .96 100 3600 7270 26 36 279 289 0 2156 151 2005 2.43 2437 2286 .411 2.284 1.281 1.191 1.281
17 316 578 162 194 154 384 319 590 167 201 157 396 0 0 87 170 46 56 90 90 75 90 538 553 .401 2.494 2.522 2.317 2.341 1.956 32 209 2.562 .78 70 3760 7280 28 35 296 303 0 470 158 312 2.027 480 322 .493 2.051 1.02 1.036 1.02
18 347 541 156 194 191 347 369 532 162 198 213 338 0 0 119 198 43 51 87 93 75 87 538 551 .55 1.817 1.587 1.706 1.802 1.552 32 172 1.892 .87 60 3890 7280 29 35 310 316 0 440 158 282 1.477 433 275 .677 1.29 .563 .368 .563
19 566 915 179 189 387 726 622 992 177 211 443 803 0 0 231 373 53 88 87 93 81 93 1113 1246 .533 1.876 1.813 2.024 1.839 1.811 32 216 1.867 .92 70 4050 7280 28 35 325 332 0 744 154 590 1.525 807 653 .656 1.474 .609 .559 .609
20 317 517 165 185 152 332 331 527 168 197 166 342 0 0 109 124 37 53 84 96 71 93 484 508 .458 2.184 2.06 2.424 1.961 2.366 32 197 2.623 .69 70 4200 7280 28 35 340 347 0 420 150 270 1.776 428 278 .563 1.675 .828 .744 .828

Total number of rows: 43008

Table truncated, full table size 9354 Kbytes.




Supplementary data files not provided
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