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Sample GSM81262 Query DataSets for GSM81262
Status Public on Nov 01, 2005
Title 8902
Sample type RNA
 
Channel 1
Source name Stratagene Universal Human Reference RNA
Organism Homo sapiens
Characteristics Stratagene Universal Human Reference RNA
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name 8902 Total RNA
Organism Homo sapiens
Characteristics 8902 Total RNA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Kidney, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49614.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 GPL3031
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
1 196 75 79 78 117 -3 204 67 83 117 125 -11 0 0 64 42 31 295 86 0 80 0 114 114 null null null .361 .406 4.392 52 270 10.906 .25 80 1420 5790 51 59 22 30 0 74 77 -3 null 66 -11 null null null null
2 254 98 81 74 173 24 256 91 83 92 175 17 0 0 63 57 22 83 98 13 98 1 197 192 7.208 .139 .097 .276 .257 2.673 52 275 .138 .15 80 1570 5800 52 60 37 45 0 97 73 24 .137 90 17 7.312 .096 -2.87 -3.384
3 1501 945 80 80 1421 865 1455 921 81 86 1375 841 0 0 430 284 20 45 100 100 100 100 2286 2216 1.643 .609 .612 .602 .603 1.478 52 254 .575 .92 80 1720 5800 52 60 52 60 0 932 79 853 .6 908 829 1.667 .603 -.737 -.73
4 109 93 82 80 27 13 110 86 83 87 28 6 0 0 29 49 18 48 61 21 36 7 40 34 2.077 .481 .214 1.722 1.379 5.313 52 264 -1 -1 80 1860 5790 51 59 66 74 0 92 79 13 .475 85 6 2.107 .211 -1.075 -2.243
5 93 68 81 72 12 -4 92 61 83 82 11 -11 0 0 21 40 18 47 36 11 11 1 8 0 null null null 1.705 1.292 2.216 52 254 .017 .03 80 2010 5790 51 59 81 89 0 67 71 -4 null 60 -11 null null null null
6 139 90 83 74 56 16 138 84 85 85 55 10 0 0 45 58 18 48 78 21 61 13 72 65 3.5 .286 .182 1.191 .718 5.352 52 264 .051 .03 80 2150 5790 51 59 95 103 0 89 73 16 .282 83 10 3.551 .179 -1.828 -2.48
7 159 86 84 77 75 9 164 74 85 87 80 -3 0 0 46 47 19 46 82 23 75 5 84 77 8.333 .12 null .621 .527 4.263 52 274 -1 -1 80 2300 5790 51 59 110 118 0 85 76 9 .118 73 -3 8.454 null -3.08 null
8 316 184 85 78 231 106 307 184 86 85 222 106 0 0 77 96 20 47 100 73 100 53 337 328 2.179 .459 .477 .39 .483 2.873 52 242 .536 .53 80 2450 5790 51 59 125 133 0 181 77 104 .452 181 104 2.211 .471 -1.145 -1.087
9 192 159 84 80 108 79 190 146 87 89 106 66 0 0 42 64 26 50 96 62 93 33 187 172 1.367 .731 .623 .667 .699 2.391 80 378 1.339 .46 100 2590 5790 50 60 138 148 0 157 79 78 .721 144 65 1.387 .614 -.472 -.704
10 127 76 87 86 40 -10 121 71 87 96 34 -15 0 0 30 40 18 53 75 3 44 0 30 19 null null null .873 .746 3.858 52 232 -1 -1 80 2740 5790 51 59 154 162 0 75 85 -10 null 70 -15 null null null null
11 538 521 87 86 451 435 544 491 95 109 457 405 0 0 140 201 73 152 98 96 95 68 886 862 1.037 .965 .886 .935 .922 1.661 80 350 1.027 .83 100 2890 5790 50 60 168 178 0 514 85 429 .951 484 399 1.052 .874 -.073 -.195
12 3173 4733 89 86 3084 4647 3038 4727 103 121 2949 4641 0 0 984 1482 112 230 100 100 100 100 7731 7590 .664 1.507 1.574 1.503 1.551 1.279 80 316 1.532 .95 100 3040 5800 51 61 183 193 0 4666 85 4581 1.485 4660 4575 .673 1.551 .571 .634
13 105 119 86 88 19 31 104 117 87 94 18 29 0 0 23 50 20 50 46 42 15 7 50 47 .613 1.632 1.611 2.331 1.979 2.334 52 242 11.508 .14 80 3170 5780 50 58 197 205 0 117 87 31 1.608 115 29 .622 1.588 .686 .667
14 92 133 91 89 1 44 90 122 89 97 -1 33 0 0 24 64 19 57 13 36 7 17 45 32 .023 44 null 3.15 3.167 4.734 52 274 56.848 .04 80 3320 5780 50 58 212 220 0 131 88 43 43.374 120 33 .023 null 5.439 null
15 113 134 91 84 22 50 112 123 91 99 21 39 0 0 24 67 21 57 48 40 13 19 72 60 .44 2.273 1.857 1.567 1.648 5.41 52 264 11.203 .2 80 3470 5780 50 58 227 235 0 132 83 49 2.24 121 38 .446 1.831 1.164 .872
16 3270 3841 90 93 3180 3748 3210 3645 93 102 3120 3552 0 0 987 1026 25 55 100 100 100 100 6928 6672 .848 1.179 1.138 1.208 1.182 1.327 80 358 1.157 .96 100 3620 5790 50 60 241 251 0 3786 92 3695 1.162 3593 3501 .861 1.122 .216 .166
17 182 419 90 97 92 322 172 396 94 105 82 299 0 0 44 159 28 62 98 96 80 88 414 381 .286 3.5 3.646 3.364 3.783 2.197 52 300 4.273 .65 90 3760 5780 49 58 255 264 0 413 96 317 3.45 390 295 .29 3.594 1.787 1.846
18 99 231 92 90 7 141 102 219 95 101 10 129 0 0 21 115 23 54 21 75 1 55 148 139 .05 20.143 12.9 5.588 6.9 3.94 52 254 27.951 .15 80 3910 5780 50 58 271 279 0 228 89 139 19.856 216 127 .05 12.716 4.312 3.669
19 2066 430 94 85 1972 345 2019 411 97 97 1925 326 0 0 436 177 27 52 100 96 100 95 2317 2251 5.716 .175 .169 .159 .167 1.667 80 332 .159 .82 100 4060 5780 49 59 285 295 0 424 84 340 .172 405 321 5.799 .167 -2.536 -2.583
20 760 617 95 91 665 526 780 600 115 120 685 509 0 0 179 209 102 132 97 96 95 90 1191 1194 1.264 .791 .743 .754 .782 1.597 120 428 .831 .89 120 4210 5780 48 60 299 311 0 608 90 519 .78 591 502 1.283 .732 -.359 -.449

Total number of rows: 41472

Table truncated, full table size 8802 Kbytes.




Supplementary data files not provided
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