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Sample GSM94490 Query DataSets for GSM94490
Status Public on Feb 01, 2006
Title PKT001 Conventional/granular RCC III
Sample type RNA
 
Channel 1
Source name crd
Organism Homo sapiens
Characteristics crd
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name PKT001
Organism Homo sapiens
Characteristics PKT001
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Kidney, primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2000-05/6267.gif
Data processing VALUE is Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Jan 30, 2006
Last update date Sep 22, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) array@genome.stanford.edu
Phone 650-498-6012
URL http://genome-www5.stanford.edu/
Department Stanford University, School of Medicine
Street address 300 Pasteur Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL3000
Series (1)
GSE4125 Renal Cell Carcinoma

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
VALUE 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
LOG_RAT2N_MEDIAN 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 VALUE LOG_RAT2N_MEDIAN
1 2190 4464 273 584 1917 3880 null null 285 605 null null null null null null null null 100 100 null null null null .494 2.024 null null 1.999 null 52 326 1.807 .93 null null null 83 92 39 48 0 4650 608 4042 2.109 null null .474 null 1.076 null
2 1521 2542 296 570 1225 1972 null null 299 645 null null null null null null null null 96 100 null null null null .621 1.61 null null 1.681 null 52 254 1.235 .83 null null null 83 91 55 63 0 2647 593 2054 1.677 null null .596 null .746 null
3 1825 1211 289 598 1536 613 null null 304 736 null null null null null null null null 96 76 null null null null 2.506 .399 null null .392 null 80 349 .288 .52 null null null 83 93 69 79 0 1261 622 639 .416 null null 2.404 null -1.265 null
4 896 1731 275 518 621 1213 null null 294 567 null null null null null null null null 96 100 null null null null .512 1.953 null null 2.06 null 52 302 1.453 .8 null null null 82 91 84 93 0 1803 539 1264 2.035 null null .491 null 1.025 null
5 6770 6627 316 723 6454 5904 null null 333 894 null null null null null null null null 100 100 null null null null 1.093 .915 null null .931 null 80 370 .84 .93 null null null 82 92 100 110 0 6903 753 6150 .953 null null 1.049 null -.07 null
6 1919 1924 332 682 1587 1242 null null 347 827 null null null null null null null null 100 96 null null null null 1.278 .783 null null .758 null 80 334 .593 .74 null null null 82 92 115 125 0 2004 710 1294 .815 null null 1.226 null -.294 null
7 578 598 288 530 290 68 null null 299 559 null null null null null null null null 70 20 null null null null 4.265 .234 null null .472 null 80 353 null 0 null null null 81 91 130 140 0 622 552 70 .241 null null 4.143 null -2.051 null
8 731 1559 279 449 452 1110 null null 291 462 null null null null null null null null 100 96 null null null null .407 2.456 null null 2.684 null 52 254 1.792 .73 null null null 83 91 146 154 0 1623 467 1156 2.558 null null .391 null 1.355 null
9 31030 4792 259 431 30771 4361 null null 280 455 null null null null null null null null 100 100 null null null null 7.056 .142 null null .135 null 52 302 .132 .94 null null null 82 91 159 168 0 4991 448 4543 .148 null null 6.773 null -2.76 null
10 2706 483 253 425 2453 58 null null 274 458 null null null null null null null null 98 19 null null null null 42.293 .024 null null .064 null 52 323 .006 .04 null null null 81 90 174 183 0 503 442 61 .025 null null 40.213 null -5.33 null
11 1291 1598 276 410 1015 1188 null null 283 416 null null null null null null null null 100 100 null null null null .854 1.17 null null 1.118 null 52 322 1.05 .87 null null null 82 91 190 199 0 1664 427 1237 1.219 null null .821 null .285 null
12 6837 3382 288 422 6549 2960 null null 299 455 null null null null null null null null 100 100 null null null null 2.213 .452 null null .443 null 52 242 .42 .93 null null null 83 91 206 214 0 3522 439 3083 .471 null null 2.124 null -1.087 null
13 6268 6743 272 440 5996 6303 null null 283 465 null null null null null null null null 96 98 null null null null .951 1.051 null null 1.069 null 80 369 .917 .95 null null null 82 92 220 230 0 7023 458 6565 1.095 null null .913 null .131 null
14 36494 13120 282 505 36212 12615 null null 321 542 null null null null null null null null 100 100 null null null null 2.871 .348 null null .347 null 52 292 .326 .96 null null null 82 91 235 244 0 13666 526 13140 .363 null null 2.756 null -1.463 null
15 1509 26992 271 441 1238 26551 null null 305 459 null null null null null null null null 95 100 null null null null .047 21.447 null null 20.79 null 80 380 13.378 .77 null null null 82 92 249 259 0 28116 459 27657 22.34 null null .045 null 4.482 null
16 4589 1888 263 425 4326 1463 null null 269 448 null null null null null null null null 100 100 null null null null 2.957 .338 null null .326 null 52 254 .315 .91 null null null 83 91 266 274 0 1966 442 1524 .352 null null 2.839 null -1.505 null
17 16596 16389 272 509 16324 15880 null null 288 559 null null null null null null null null 100 100 null null null null 1.028 .973 null null .957 null 80 406 .932 .97 null null null 82 92 280 290 0 17071 530 16541 1.013 null null .987 null .019 null
18 999 1822 312 611 687 1211 null null 334 703 null null null null null null null null 84 92 null null null null .567 1.763 null null 1.742 null 52 338 1.297 .77 null null null 80 89 296 305 -100 1897 636 1261 1.836 null null .545 null .876 null
19 12482 18330 299 562 12183 17768 null null 319 619 null null null null null null null null 100 100 null null null null .686 1.458 null null 1.46 null 52 311 1.39 .95 null null null 82 91 312 321 0 19093 585 18508 1.519 null null .658 null .603 null
20 2500 3590 283 593 2217 2997 null null 292 623 null null null null null null null null 100 100 null null null null .74 1.352 null null 1.371 null 52 289 1.244 .91 null null null 82 91 327 336 0 3739 617 3122 1.408 null null .71 null .494 null

Total number of rows: 24192

Table truncated, full table size 5823 Kbytes.




Supplementary data files not provided
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