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Sample GSM81345 Query DataSets for GSM81345
Status Public on Nov 01, 2005
Title 9935
Sample type RNA
 
Channel 1
Source name Stratagene universal RNA
Organism Homo sapiens
Characteristics Stratagene universal RNA
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name 9935 total RNA
Organism Homo sapiens
Characteristics 9935 total RNA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Kidney, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/44920.gif; format: GIF
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 Oct 31, 2005
Last update date Oct 21, 2011
Contact name Hongjuan Zhao
E-mail(s) [email protected]
Phone 650-498-4922
Fax 650-723-0765
Organization name Stanford University
Department Urology, Edwards Building R116
Street address 300 Pasteur Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL3028
Series (1)
GSE3538 Conventional renal cell carcinomas
Relations
Reanalyzed by GSE33093

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 94 136 78 117 16 19 93 125 79 127 15 8 0 0 23 63 14 56 50 26 25 7 35 23 .842 1.188 .533 2.168 2.625 5.016 52 254 20.155 .019 80 1560 6570 41 49 36 44 -50 154 132 22 1.344 142 9 .744 .604 .427 -.728
2 224 335 79 126 145 209 217 355 80 132 138 229 0 0 42 129 15 57 100 87 100 75 354 367 .694 1.441 1.659 1.115 1.429 2.836 32 177 2.15 .509 70 1680 6590 43 50 48 55 0 379 143 237 1.632 402 259 .613 1.879 .706 .91
3 351 231 81 126 270 105 385 211 83 133 304 85 0 0 186 119 17 59 88 59 76 42 375 389 2.571 .389 .28 .472 .468 3.256 52 302 .433 .354 80 1820 6580 42 50 62 70 0 262 143 119 .44 239 96 2.271 .317 -1.184 -1.66
4 110 123 80 128 30 -5 97 122 82 137 17 -6 0 0 39 52 17 58 50 17 38 0 25 11 null null null 1.336 1.012 4.633 52 290 -1 0 80 2000 6570 41 49 80 88 -50 139 145 -6 null 138 -7 null null null null
5 234 250 80 134 154 116 235 236 82 136 155 102 0 0 52 104 16 58 100 71 100 40 270 257 1.328 .753 .658 .757 .734 2.563 32 207 1.482 .231 70 2120 6580 42 49 92 99 0 283 152 131 .853 267 115 1.173 .745 -.23 -.425
6 110 121 80 130 30 -9 108 107 81 136 28 -23 0 0 30 54 16 59 63 13 48 3 21 5 null null null 1.01 1.455 6.057 52 278 .036 .003 80 2290 6570 41 49 109 117 -50 137 147 -10 null 121 -26 null null null null
7 136 144 80 127 56 17 127 142 82 136 47 15 0 0 61 72 16 62 63 17 53 9 73 62 3.294 .304 .319 1.058 .954 5.868 52 256 2.938 .072 80 2440 6570 41 49 124 132 -50 163 144 19 .344 161 17 2.91 .361 -1.541 -1.469
8 145 141 81 126 64 15 150 137 83 132 69 11 0 0 46 53 18 62 82 25 63 1 79 80 4.267 .234 .159 .81 .923 3.598 52 256 3.981 .039 80 2580 6570 41 49 138 146 -50 160 143 17 .265 155 12 3.769 .18 -1.914 -2.47
9 180 152 81 132 99 20 198 140 82 135 117 8 0 0 62 67 18 54 84 30 80 9 119 125 4.95 .202 .068 .569 .668 4.311 52 256 .948 .038 80 2730 6570 41 49 153 161 -50 172 149 23 .229 158 9 4.373 .077 -2.128 -3.691
10 143 146 79 123 64 23 144 136 82 128 65 13 0 0 26 53 20 53 90 25 86 3 87 78 2.783 .359 .2 .637 .709 2.582 52 224 4.374 .04 80 2870 6570 41 49 167 175 -50 165 139 26 .407 154 15 2.458 .226 -1.297 -2.143
11 713 470 80 129 633 341 733 462 119 268 653 333 0 0 162 140 292 904 96 0 63 0 974 986 1.856 .539 .51 .517 .535 1.557 80 317 .547 .698 100 3010 6570 40 50 180 190 0 532 146 386 .61 523 377 1.64 .577 -.713 -.793
12 2924 2122 80 131 2844 1991 3670 2378 117 265 3590 2247 0 0 1501 1068 290 872 88 77 82 67 4835 5837 1.428 .7 .626 .725 .692 1.492 80 322 .696 .938 100 3150 6580 41 51 194 204 0 2402 148 2254 .793 2692 2544 1.262 .709 -.335 -.497
13 220 324 80 128 140 196 213 321 83 137 133 193 0 0 38 119 17 60 100 86 100 69 336 326 .714 1.4 1.451 1.172 1.543 2.316 52 315 2.349 .438 90 3300 6570 40 49 209 218 0 367 145 222 1.585 363 218 .631 1.643 .664 .716
14 135 159 80 125 55 34 135 159 85 131 55 34 0 0 22 58 26 59 86 28 57 9 89 89 1.618 .618 .618 1.003 1.079 2.605 52 262 9.01 .024 80 3460 6570 41 49 226 234 -50 180 142 38 .7 180 38 1.429 .7 -.515 -.515
15 135 355 79 131 56 224 133 331 82 134 54 200 0 0 23 96 17 55 96 98 84 94 280 254 .25 4 3.704 3.987 4.039 1.917 52 289 6.116 .435 90 3590 6570 40 49 238 247 0 402 148 254 4.528 375 226 .221 4.193 2.179 2.068
16 3466 2121 80 131 3386 1990 4010 2453 84 136 3930 2322 0 0 1359 865 35 57 100 100 100 98 5376 6252 1.702 .588 .591 .574 .598 1.577 80 422 .578 .888 110 3740 6570 39 50 252 263 0 2401 148 2253 .665 2777 2629 1.503 .669 -.588 -.58
17 450 419 82 133 368 286 444 406 83 135 362 273 0 0 82 134 28 56 100 96 100 92 654 635 1.287 .777 .754 .692 .742 1.842 52 233 .88 .644 80 3890 6580 42 50 269 277 0 474 151 324 .88 460 309 1.137 .854 -.185 -.228
18 106 150 80 131 26 19 105 149 83 134 25 18 0 0 18 62 19 55 59 28 26 7 45 43 1.368 .731 .72 1.751 1.779 3.208 52 255 24.787 .009 80 4040 6560 40 48 284 292 -50 170 148 22 .827 169 20 1.209 .815 -.274 -.295
19 1362 1045 79 135 1283 910 1356 1033 82 137 1277 898 0 0 244 258 17 53 100 100 100 100 2193 2175 1.41 .709 .703 .691 .725 1.337 80 355 .695 .844 110 4180 6570 39 50 296 307 0 1183 153 1030 .803 1169 1017 1.245 .796 -.317 -.329
20 549 348 79 132 470 216 541 344 82 134 462 212 0 0 79 89 17 52 100 98 100 86 686 674 2.176 .46 .459 .42 .446 1.656 80 355 .429 .519 110 4320 6570 39 50 310 321 0 394 149 245 .52 389 240 1.922 .519 -.943 -.945

Total number of rows: 41568

Table truncated, full table size 8924 Kbytes.




Supplementary data files not provided
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