NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM81373 Query DataSets for GSM81373
Status Public on Nov 01, 2005
Title 9932
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 9932 total RNA
Organism Homo sapiens
Characteristics 9932 total RNA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Kidney, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/44795.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 78 66 77 59 1 7 80 61 78 60 3 2 0 0 15 23 13 21 15 26 3 13 8 5 .143 7 .667 1.719 1.581 2.879 52 344 16.606 .004 90 2130 8330 28 37 28 37 -50 87 78 9 9.275 81 3 .108 .883 3.213 -.179
2 138 75 78 57 60 18 142 67 79 60 64 10 0 0 46 35 14 23 76 38 75 19 78 74 3.333 .3 .156 .46 .51 2.857 52 312 .317 .054 90 2270 8330 28 37 42 51 -50 99 76 24 .398 89 13 2.516 .207 -1.331 -2.272
3 209 100 74 57 135 43 117 74 77 62 43 17 0 0 257 78 15 24 65 40 57 30 178 60 3.14 .319 .395 .43 .333 3.637 52 322 .268 .553 90 2420 8330 28 37 57 66 -50 133 76 57 .422 98 23 2.369 .524 -1.245 -.933
4 88 66 74 60 14 6 85 62 76 63 11 2 0 0 22 20 15 24 38 21 17 1 20 13 2.333 .429 .182 1.105 1 4.854 52 312 19.545 .001 90 2560 8330 28 37 71 80 -50 87 80 8 .568 82 3 1.761 .241 -.816 -2.053
5 187 114 75 62 112 52 109 91 76 63 34 29 0 0 126 63 15 24 67 51 53 44 164 63 2.154 .464 .853 .615 .538 2.753 52 324 .458 .473 90 2710 8330 28 37 86 95 -50 151 82 69 .615 121 38 1.626 1.13 -.701 .177
6 80 73 74 61 6 12 80 67 75 63 6 6 0 0 16 21 14 24 26 26 11 7 18 12 .5 2 1 1.394 1.343 3.106 52 312 -1 0 90 2860 8330 28 37 101 110 -50 97 81 16 2.65 89 8 .377 1.325 1.406 .406
7 131 88 74 61 57 27 89 74 74 63 15 13 0 0 94 45 14 23 51 40 36 28 84 28 2.111 .474 .867 .643 .545 2.973 52 312 .518 .423 90 3000 8330 28 37 115 124 -50 117 81 36 .628 98 17 1.593 1.148 -.672 .2
8 133 124 74 59 59 65 114 109 74 61 40 50 0 0 56 71 14 22 78 61 59 51 124 90 .908 1.102 1.25 1.099 1.185 2.482 52 312 1.328 .531 90 3150 8330 28 37 130 139 -50 164 78 86 1.46 144 66 .685 1.656 .546 .728
9 126 92 75 61 51 31 126 86 76 62 51 25 0 0 35 36 15 22 84 53 65 32 82 76 1.645 .608 .49 .548 .615 3.519 52 312 .831 .142 90 3290 8330 28 37 144 153 -50 122 81 41 .805 114 33 1.242 .65 -.312 -.623
10 78 61 78 62 0 -1 76 59 78 63 -2 -3 0 0 16 24 13 21 15 17 7 3 -1 -5 null null null 1.596 1.061 4.808 52 313 -1 0 90 3440 8330 28 37 159 168 -50 81 82 -1 null 78 -4 null null null null
11 348 430 78 62 270 368 340 376 79 62 262 314 0 0 170 219 14 22 96 100 95 100 638 576 .734 1.363 1.198 1.494 1.332 1.688 80 358 1.356 .893 100 3590 8340 29 39 174 184 0 570 82 488 1.806 498 416 .554 1.588 .853 .667
12 1641 1530 78 62 1563 1468 1541 1338 80 64 1463 1276 0 0 698 597 15 22 100 100 100 100 3031 2739 1.065 .939 .872 .963 .96 1.226 52 288 .918 .969 90 3730 8340 29 38 188 197 0 2027 82 1945 1.244 1773 1691 .804 1.156 .316 .209
13 108 109 79 64 29 45 102 110 80 66 23 46 0 0 24 30 14 23 71 75 44 50 74 69 .644 1.552 2 1.751 1.787 2.587 52 280 2.497 .128 90 3880 8330 28 37 203 212 -50 144 85 60 2.056 146 61 .486 2.65 1.04 1.406
14 116 127 80 62 36 65 115 122 81 66 35 60 0 0 24 48 14 24 78 83 57 60 101 95 .554 1.806 1.714 1.883 1.831 2.971 120 432 2.958 .233 120 4020 8340 28 40 216 228 0 168 82 86 2.392 162 80 .418 2.271 1.258 1.184
15 121 163 77 63 44 100 122 148 79 65 45 85 0 0 25 66 20 25 82 90 63 76 144 130 .44 2.273 1.889 1.996 1.907 2.324 80 308 3.142 .432 100 4170 8350 30 40 232 242 0 216 83 133 3.011 196 113 .332 2.503 1.59 1.324
16 2614 1317 78 65 2536 1252 2854 1399 80 66 2776 1334 0 0 1032 518 20 25 96 98 96 98 3788 4110 2.026 .494 .481 .523 .503 1.496 80 311 .487 .949 100 4320 8350 30 40 247 257 0 1745 86 1659 .654 1854 1768 1.529 .637 -.612 -.651
17 394 707 78 62 316 645 386 712 80 65 308 650 0 0 110 186 14 24 100 100 100 100 961 958 .49 2.041 2.11 2.079 2.029 1.282 80 396 2.067 .914 110 4460 8340 28 39 260 271 0 937 82 855 2.705 943 861 .37 2.796 1.435 1.484
18 73 69 78 63 -5 6 72 63 79 67 -6 0 0 0 11 27 15 24 7 25 0 9 1 -6 null null null 1.588 1.235 3.974 52 312 13.509 .012 90 4610 8330 28 37 276 285 -50 91 83 8 null 83 0 null null null null
19 861 414 76 65 785 349 870 415 77 66 794 350 0 0 175 96 15 23 100 100 100 100 1134 1144 2.249 .445 .441 .439 .436 1.281 52 289 .441 .893 90 4750 8340 29 38 290 299 0 549 86 462 .589 550 464 1.698 .584 -.763 -.776
20 382 175 78 62 304 113 428 168 80 65 350 106 0 0 142 62 16 21 100 94 100 86 417 456 2.69 .372 .303 .369 .367 1.73 52 301 .35 .641 90 4890 8340 29 38 304 313 0 232 82 150 .493 223 140 2.03 .401 -1.022 -1.317

Total number of rows: 43008

Table truncated, full table size 8846 Kbytes.




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