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Sample GSM81370 Query DataSets for GSM81370
Status Public on Nov 01, 2005
Title 0026
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 00026 total RNA
Organism Homo sapiens
Characteristics 00026 total RNA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Kidney, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/44792.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 GPL3025
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 76 67 81 65 -5 2 75 66 81 66 -6 1 0 0 11 18 10 17 9 17 1 5 -3 -5 null null null 1.661 2 2.708 52 345 8.381 .024 90 2140 8630 34 43 21 30 -50 82 79 2 null 81 1 null null null null
2 207 87 79 67 128 20 200 90 79 67 121 23 0 0 54 22 11 17 100 57 100 26 148 144 6.4 .156 .19 .161 .184 2.68 52 301 .154 .109 90 2290 8630 34 43 36 45 0 106 82 24 .191 110 28 5.233 .232 -2.388 -2.105
3 303 193 78 64 225 129 220 164 78 65 142 100 0 0 213 120 10 18 94 78 88 71 354 242 1.744 .573 .704 .573 .597 2.19 52 254 .552 .857 80 2430 8630 35 43 51 59 0 236 78 158 .701 201 122 1.426 .861 -.512 -.215
4 89 65 77 65 12 0 88 63 77 66 11 -2 0 0 14 15 10 18 50 7 28 3 12 9 null null null .799 .875 4.416 52 300 .065 .004 90 2580 8630 34 43 65 74 -50 79 79 0 null 77 -2 null null null null
5 248 212 76 65 172 147 252 224 76 66 176 159 0 0 97 85 10 17 100 96 100 90 319 335 1.17 .855 .903 .834 .842 1.54 52 264 .847 .886 80 2720 8630 35 43 80 88 0 259 79 180 1.045 274 194 .957 1.105 .064 .144
6 76 72 76 64 0 8 75 71 76 66 -1 7 0 0 10 19 10 17 15 36 1 3 8 6 null null null 1.823 1.993 4.233 52 300 .052 .005 90 2870 8630 34 43 94 103 -50 88 78 10 null 87 9 null null null null
7 174 235 76 65 98 170 168 216 77 66 92 151 0 0 69 112 10 18 88 92 86 84 268 243 .576 1.735 1.641 1.751 1.792 1.5 52 264 1.778 .84 80 3010 8630 35 43 109 117 0 287 79 208 2.122 264 185 .471 2.007 1.085 1.005
8 139 93 75 64 64 29 137 89 75 67 62 25 0 0 32 25 10 19 98 55 94 34 93 87 2.207 .453 .403 .386 .404 2.504 52 301 .556 .289 90 3160 8630 34 43 123 132 0 114 78 35 .554 109 31 1.804 .493 -.852 -1.02
9 147 105 76 67 71 38 146 104 77 68 70 37 0 0 22 28 9 18 100 71 100 50 109 107 1.868 .535 .529 .439 .553 2.407 52 305 .696 .364 90 3300 8620 33 42 137 146 0 128 82 46 .655 127 45 1.528 .646 -.611 -.629
10 76 65 78 68 -2 -3 74 66 78 68 -4 -2 0 0 12 14 10 18 17 9 1 0 -5 -6 null null null 1.358 1.432 3.145 52 305 6.782 .032 90 3450 8620 33 42 152 161 -50 79 83 -4 null 81 -2 null null null null
11 463 360 78 68 385 292 488 365 78 69 410 297 0 0 137 112 10 18 100 100 100 100 677 707 1.318 .758 .724 .755 .768 1.239 80 388 .761 .935 110 3600 8630 33 44 166 177 0 440 83 357 .928 446 363 1.078 .886 -.108 -.175
12 1263 2817 77 70 1186 2747 1348 2860 77 71 1271 2790 0 0 583 1364 10 18 100 100 100 100 3933 4061 .432 2.316 2.195 2.327 2.325 1.153 80 328 2.329 .986 100 3740 8630 34 44 181 191 0 3445 86 3360 2.833 3498 3412 .353 2.685 1.502 1.425
13 108 204 77 69 31 135 107 200 77 71 30 131 0 0 17 44 10 18 90 100 75 100 166 161 .23 4.355 4.367 4.541 4.386 1.57 52 245 4.564 .573 90 3880 8630 34 43 195 204 0 250 84 165 5.326 245 160 .188 5.341 2.413 2.417
14 109 195 80 72 29 123 108 190 80 73 28 118 0 0 16 55 10 18 87 98 62 96 152 146 .236 4.241 4.214 4.598 4.373 2.192 120 445 5.249 .441 120 4020 8630 33 45 208 220 0 238 88 150 5.187 232 144 .193 5.154 2.375 2.366
15 121 237 78 71 43 166 121 230 78 72 43 159 0 0 21 54 10 19 92 100 88 98 209 202 .259 3.86 3.698 4.109 3.968 1.757 80 336 4.037 .653 110 4180 8640 34 45 224 235 0 290 87 203 4.722 281 194 .212 4.523 2.239 2.177
16 2572 1987 78 70 2494 1917 2622 1965 79 73 2544 1895 0 0 407 306 10 20 100 100 100 100 4411 4439 1.301 .769 .745 .77 .77 1.108 80 347 .768 .981 110 4320 8630 33 44 238 249 0 2430 86 2345 .94 2403 2318 1.064 .911 -.089 -.134
17 354 580 81 72 273 508 349 606 82 74 268 534 0 0 112 153 11 19 100 100 100 100 781 802 .537 1.861 1.993 1.941 1.877 1.281 120 437 1.814 .921 120 4470 8630 33 45 253 265 0 709 88 621 2.276 741 653 .439 2.437 1.186 1.285
18 82 75 84 71 -2 4 81 72 84 74 -3 1 0 0 11 18 11 19 5 21 1 3 2 -2 null null null 1.416 1.6 3.409 52 262 -1 0 90 4620 8620 33 42 269 278 -50 92 87 5 null 88 1 null null null null
19 827 353 81 72 746 281 861 362 82 75 780 290 0 0 185 75 10 20 100 100 100 100 1027 1070 2.655 .377 .372 .377 .385 1.221 80 341 .371 .932 100 4760 8630 34 44 283 293 0 432 88 344 .461 443 355 2.171 .455 -1.118 -1.137
20 313 208 89 76 224 132 308 213 92 78 219 137 0 0 71 49 16 21 100 98 100 92 356 356 1.697 .589 .626 .566 .574 1.417 80 357 .597 .816 110 4910 8630 33 44 297 308 0 254 93 161 .721 261 168 1.387 .765 -.472 -.386

Total number of rows: 43008

Table truncated, full table size 8838 Kbytes.




Supplementary data files not provided
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