NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM81358 Query DataSets for GSM81358
Status Public on Nov 01, 2005
Title 9022
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 9022 Total RNA
Organism Homo sapiens
Characteristics 9022 Total RNA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Kidney, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/45444.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 GPL3029
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
1 580 258 224 117 356 141 543 256 233 122 319 139 0 0 172 78 64 53 96 82 92 63 497 458 2.525 .396 .436 .364 .41 2.219 52 247 .31 .55 80 2010 5540 38 46 29 37 0 228 103 125 .35 226 123 2.855 .385 -1.513 -1.376
2 1604 347 230 122 1374 225 1580 326 243 128 1350 204 0 0 679 140 73 60 100 86 96 80 1599 1554 6.107 .164 .151 .16 .161 2.281 52 228 .143 .76 80 2150 5540 38 46 43 51 0 307 108 199 .145 288 180 6.904 .134 -2.788 -2.903
3 3246 3300 234 119 3012 3181 3854 3481 241 131 3620 3362 0 0 2211 2055 73 67 98 100 96 98 6193 6982 .947 1.056 .929 1.259 1.074 1.986 80 360 1 .94 100 2290 5540 37 47 56 66 0 2919 105 2813 .934 3079 2974 1.071 .821 -.098 -.284
4 677 183 227 119 450 64 622 189 233 128 395 70 0 0 388 71 58 54 82 53 75 26 514 465 7.031 .142 .177 .209 .205 3.871 52 244 .088 .38 80 2440 5540 38 46 72 80 -50 162 105 57 .126 167 62 7.95 .157 -2.991 -2.674
5 1392 4016 230 115 1162 3901 1453 4186 230 123 1223 4071 0 0 381 760 63 53 100 100 100 100 5063 5294 .298 3.357 3.329 3.531 3.204 1.507 52 302 3.683 .89 90 2580 5540 37 46 85 94 0 3552 102 3450 2.969 3702 3601 .337 2.944 1.57 1.558
6 785 288 219 123 566 165 751 282 220 126 532 159 0 0 163 85 64 54 100 92 100 75 731 691 3.43 .292 .299 .266 .275 1.952 52 254 .258 .67 80 2730 5540 38 46 101 109 0 255 109 146 .258 249 141 3.878 .264 -1.955 -1.92
7 1025 2268 214 121 811 2147 1056 2243 219 130 842 2122 0 0 231 526 60 56 100 100 98 100 2958 2964 .378 2.647 2.52 2.699 2.653 1.451 52 255 2.747 .92 80 2870 5540 38 46 115 123 0 2006 107 1899 2.341 1984 1877 .427 2.229 1.227 1.156
8 1159 969 234 121 925 848 1162 1012 238 128 928 891 0 0 198 214 64 55 100 100 100 100 1773 1819 1.091 .917 .96 .908 .882 1.424 52 255 .912 .88 80 3020 5540 38 46 130 138 0 857 107 750 .811 895 788 1.233 .849 -.303 -.236
9 1204 1040 231 125 973 915 1248 1056 234 129 1017 931 0 0 256 209 66 57 100 100 98 100 1888 1948 1.063 .94 .915 .977 .934 1.565 80 376 .947 .88 110 3170 5540 36 47 143 154 0 920 111 809 .832 934 823 1.202 .81 -.266 -.305
10 935 198 228 122 707 76 957 181 235 128 729 59 0 0 181 80 67 60 100 48 98 22 783 788 9.303 .107 .081 .106 .127 2.699 80 275 .098 .45 100 3320 5540 37 47 159 169 0 175 108 67 .095 160 52 10.518 .072 -3.395 -3.804
11 2494 2551 221 121 2273 2430 2819 2929 229 127 2598 2808 0 0 1097 1034 70 55 99 100 99 100 4703 5406 .935 1.069 1.081 1.123 1.025 1.853 120 378 1.043 .91 120 3470 5540 36 48 173 185 0 2256 107 2149 .946 2591 2484 1.058 .956 -.081 -.065
12 7547 33392 224 124 7323 33268 9098 41144 232 127 8874 41020 0 0 3734 15798 72 51 100 100 100 100 40591 49894 .22 4.543 4.622 4.685 4.511 1.63 120 404 4.645 .95 120 3610 5540 36 48 187 199 0 29533 110 29424 4.018 36390 36280 .249 4.088 2.006 2.032
13 674 1511 229 122 445 1389 707 1635 240 128 478 1513 0 0 211 412 75 51 94 100 90 100 1834 1991 .32 3.121 3.165 3.261 3.175 1.643 120 417 3.17 .86 120 3760 5540 36 48 202 214 0 1336 108 1228 2.761 1446 1338 .362 2.8 1.465 1.485
14 558 720 221 121 337 599 576 728 230 126 355 607 0 0 135 181 67 51 95 100 90 100 936 962 .563 1.777 1.71 1.887 1.846 1.914 80 348 1.921 .78 110 3900 5540 36 47 216 227 0 637 107 530 1.572 644 537 .636 1.512 .653 .597
15 540 2835 231 119 309 2716 566 2912 236 125 335 2793 0 0 155 936 65 54 90 100 85 100 3025 3128 .114 8.79 8.337 9.354 8.455 2.087 120 400 9.27 .78 120 4060 5540 36 48 232 244 0 2507 105 2402 7.774 2576 2470 .129 7.374 2.959 2.882
16 16319 14535 224 128 16095 14407 20929 18446 234 134 20705 18318 0 0 9324 6973 67 60 100 100 100 100 30502 39023 1.117 .895 .885 .974 .87 1.653 120 396 .837 .94 120 4200 5540 36 48 246 258 0 12855 113 12742 .792 16315 16201 1.263 .782 -.337 -.354
17 1868 3506 228 122 1640 3384 1844 3479 238 132 1616 3357 0 0 292 585 64 61 100 100 100 100 5024 4973 .485 2.063 2.077 2.066 2.087 1.262 80 373 2.256 .91 110 4350 5540 36 47 261 272 0 3101 108 2993 1.825 3077 2969 .548 1.837 .868 .878
18 628 284 231 126 397 158 621 283 238 133 390 157 0 0 113 91 62 59 100 90 100 57 555 547 2.513 .398 .403 .346 .361 2.05 52 256 .378 .63 90 4500 5540 37 46 277 286 0 251 111 140 .352 250 139 2.841 .356 -1.506 -1.49
19 5234 4357 231 124 5003 4233 5319 4433 236 130 5088 4309 0 0 1256 1059 63 53 100 100 100 100 9236 9397 1.182 .846 .847 .846 .847 1.345 120 421 .837 .96 120 4640 5540 36 48 290 302 0 3854 110 3744 .748 3921 3811 1.336 .749 -.418 -.417
20 2594 2448 236 122 2358 2326 2563 2384 243 130 2327 2262 0 0 492 502 69 57 100 100 100 100 4684 4589 1.014 .986 .972 .987 .992 1.289 80 345 .975 .94 110 4780 5540 36 47 304 315 0 2165 108 2057 .872 2109 2001 1.146 .86 -.197 -.218

Total number of rows: 41568

Table truncated, full table size 9328 Kbytes.




Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap