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Sample GSM39918 Query DataSets for GSM39918
Status Public on Feb 21, 2005
Title Bladder 1678
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Bladder 1678
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-01/24780.gif
 
Submission date Jan 26, 2005
Last update date Nov 22, 2005
Contact name Jonathan Pollack
E-mail(s) [email protected]
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
1 294 164 138 104 156 60 288 160 140 106 150 56 0 0 81 40 30 19 92 82 86 67 216 206 2.6 .385 .373 .357 .444 2.358 52 278 .323 .68 80 1600 8120 40 48 40 48 0 171 108 63 .401 167 58 2.496 .389 -1.32 -1.363 -1.32
2 246 141 140 115 106 26 249 133 143 116 109 18 0 0 76 30 31 19 85 46 71 30 132 127 4.077 .245 .165 .301 .286 4.126 80 346 .129 .3 100 1750 8120 39 49 54 64 0 147 120 27 .256 139 19 3.914 .172 -1.969 -2.539 -1.969
3 557 962 139 118 418 844 582 1024 142 118 443 906 0 0 244 378 30 20 96 100 95 100 1262 1349 .495 2.019 2.045 2.21 2.007 1.555 80 355 1.951 .93 100 1880 8120 39 49 67 77 0 1002 123 879 2.103 1067 944 .475 2.13 1.073 1.091 1.073
4 1953 2945 143 115 1810 2830 2016 3061 146 116 1873 2946 0 0 1012 1479 31 20 98 100 98 100 4640 4819 .64 1.564 1.573 1.652 1.572 1.568 80 396 1.548 .96 100 2030 8120 39 49 82 92 0 3068 120 2948 1.629 3189 3069 .614 1.638 .704 .712 .704
5 310 304 145 113 165 191 334 313 148 113 189 200 0 0 95 86 33 20 88 96 82 94 356 389 .864 1.158 1.058 1.225 1.238 1.725 52 321 1.054 .83 90 2180 8130 40 49 97 106 0 317 118 199 1.206 326 208 .829 1.102 .27 .141 .27
6 259 156 152 114 107 42 264 163 167 119 112 49 0 0 80 28 62 29 81 78 46 25 149 161 2.548 .393 .438 .385 .381 2.787 32 206 .321 .53 70 2330 8130 41 48 113 120 0 163 119 44 .409 170 51 2.446 .456 -1.29 -1.134 -1.29
7 339 396 158 120 181 276 355 422 185 128 197 302 0 0 101 109 90 32 84 96 53 94 457 499 .656 1.525 1.533 1.45 1.596 2.385 52 293 1.423 .81 90 2480 8120 39 48 127 136 0 413 125 288 1.588 440 315 .63 1.597 .668 .675 .668
8 1515 2889 149 121 1366 2768 1594 3015 157 123 1445 2894 0 0 755 1313 53 21 97 100 96 100 4134 4339 .493 2.026 2.003 2.279 2.017 1.569 80 331 1.953 .97 100 2610 8120 39 49 140 150 0 3009 126 2883 2.111 3141 3015 .474 2.086 1.078 1.061 1.078
9 554 891 147 121 407 770 566 975 148 122 419 854 0 0 186 287 30 19 98 100 96 100 1177 1273 .529 1.892 2.038 1.98 1.981 1.443 52 322 1.922 .93 90 2760 8120 39 48 155 164 0 928 126 802 1.971 1016 890 .507 2.123 .979 1.086 .979
10 275 272 146 121 129 151 274 280 148 122 128 159 0 0 68 68 31 18 92 98 84 98 280 287 .854 1.171 1.242 1.142 1.12 1.668 52 245 1.176 .8 80 2910 8120 40 48 171 179 0 283 126 157 1.219 292 166 .82 1.294 .286 .372 .286
11 520 536 143 122 377 414 540 545 147 123 397 423 0 0 256 243 35 18 92 98 88 96 791 820 .911 1.098 1.065 1.263 1.13 1.999 52 327 1.052 .94 90 3040 8130 40 49 183 192 0 558 127 431 1.144 568 441 .874 1.11 .194 .15 .194
12 660 609 149 126 511 483 683 622 151 126 534 496 0 0 203 179 35 19 98 98 96 98 994 1030 1.058 .945 .929 1.009 .955 1.84 52 322 .949 .92 90 3200 8120 39 48 199 208 0 634 131 503 .985 648 517 1.016 .968 -.022 -.048 -.022
13 474 378 154 136 320 242 479 366 155 138 325 230 0 0 144 112 34 21 96 96 92 94 562 555 1.322 .756 .708 .722 .737 1.698 52 254 .72 .91 80 3340 8120 40 48 214 222 0 394 142 252 .788 381 240 1.269 .737 -.344 -.44 -.344
14 291 237 157 136 134 101 289 238 158 138 132 102 0 0 89 46 32 20 84 96 76 86 235 234 1.327 .754 .773 .875 .718 2.1 52 242 .569 .71 80 3490 8120 40 48 229 237 0 247 142 105 .785 248 106 1.274 .805 -.349 -.313 -.349
15 1867 3413 156 141 1711 3272 1934 3774 158 141 1778 3633 0 0 792 1500 33 21 100 100 100 100 4983 5411 .523 1.912 2.043 1.924 1.901 1.474 80 379 1.937 .97 110 3630 8120 38 49 241 252 0 3555 147 3408 1.992 3931 3784 .502 2.128 .994 1.09 .994
16 860 1196 157 140 703 1056 959 1387 158 141 802 1247 0 0 343 428 33 20 95 97 95 97 1759 2049 .666 1.502 1.555 1.687 1.534 1.72 80 353 1.418 .96 100 3770 8120 39 49 256 266 0 1246 146 1100 1.565 1445 1299 .639 1.62 .646 .696 .646
17 251 180 155 141 96 39 255 190 157 142 100 49 0 0 66 43 35 21 87 65 68 56 135 149 2.462 .406 .49 .444 .529 3.086 32 214 .353 .48 70 3930 8120 40 47 273 280 0 188 147 41 .423 198 51 2.363 .51 -1.241 -.97 -1.241
18 290 155 157 145 133 10 282 148 158 146 125 3 0 0 76 27 32 27 93 25 84 9 143 128 13.3 .075 .024 .16 .203 2.854 32 212 .077 .21 70 4070 8110 39 46 287 294 0 161 151 10 .078 154 3 12.768 .025 -3.674 -5.322 -3.674
19 523 564 154 141 369 423 499 602 157 144 345 461 0 0 189 258 34 28 96 96 96 90 792 806 .872 1.146 1.336 .905 1.07 2.181 32 192 1.237 .92 70 4220 8130 41 48 302 309 0 588 147 441 1.194 627 480 .837 1.392 .256 .477 .256
20 289 179 157 140 132 39 302 189 159 141 145 49 0 0 90 48 33 22 81 65 78 56 171 194 3.385 .295 .338 .387 .336 2.528 32 198 .303 .55 70 4360 8120 40 47 316 323 0 186 146 41 .308 197 51 3.249 .352 -1.7 -1.506 -1.7

Total number of rows: 43008

Table truncated, full table size 9199 Kbytes.




Supplementary data files not provided
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