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Sample GSM39895 Query DataSets for GSM39895
Status Public on Feb 21, 2005
Title Bladder 1004
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Bladder 1004
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-11/21776.gif
 
Submission date Jan 26, 2005
Last update date Nov 22, 2005
Contact name Jonathan Pollack
E-mail(s) [email protected]
Phone 650-736-1987
Organization name Stanford University
Department Pathology
Lab Pollack Lab
Street address 269 Campus Drive, CCSR3245A
City Stanford
State/province CA
ZIP/Postal code 94305-5176
Country USA
 
Platform ID GPL1823
Series (1)
GSE2193 Normal_human_tissues

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 same as UNF_VALUE but with flagged values removed
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
UNF_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

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 UNF_VALUE
1 815 780 255 228 560 552 811 757 263 231 556 529 0 0 303 257 80 69 94 98 92 96 1112 1085 1.014 .986 .951 1.021 .992 1.799 52 268 .897 .79 80 1240 7560 8 16 44 52 0 619 181 438 .782 601 420 1.278 .755 -.354 -.405 -.354
2 628 345 252 215 376 130 609 345 259 220 357 130 0 0 156 101 75 69 100 76 94 40 506 487 2.892 .346 .364 .322 .342 2.151 52 256 .305 .5 80 1390 7560 8 16 59 67 0 274 171 103 .274 274 103 3.644 .289 -1.866 -1.791 -1.866
3 2349 6677 250 207 2099 6470 2407 7073 256 214 2157 6866 0 0 652 1644 73 73 100 100 100 100 8569 9023 .324 3.082 3.183 3.15 3.096 1.232 52 256 3.077 .95 80 1530 7560 8 16 73 81 0 5299 164 5135 2.446 5613 5449 .409 2.526 1.291 1.337 1.291
4 6868 10038 252 180 6616 9858 6687 9713 253 192 6435 9533 0 0 2706 3849 71 71 100 100 100 100 16474 15968 .671 1.49 1.481 1.525 1.485 1.327 52 270 1.483 .96 80 1680 7560 8 16 88 96 0 7967 143 7824 1.183 7709 7566 .846 1.176 .242 .234 .242
5 886 997 254 194 632 803 864 1105 263 202 610 911 0 0 262 400 77 67 100 100 100 96 1435 1521 .787 1.271 1.493 1.158 1.367 1.924 32 213 1.336 .86 70 1820 7560 8 15 102 109 0 791 154 637 1.008 877 723 .992 1.185 .012 .245 .012
6 659 601 263 230 396 371 627 601 274 237 364 371 0 0 194 144 83 78 94 96 88 92 767 735 1.067 .937 1.019 .97 .965 1.839 52 287 .808 .77 80 1970 7560 8 16 117 125 0 477 183 294 .744 477 294 1.345 .809 -.428 -.306 -.428
7 1340 1901 268 223 1072 1678 1324 1873 269 231 1056 1650 0 0 302 351 74 71 100 100 100 100 2750 2706 .639 1.565 1.563 1.597 1.561 1.421 52 230 1.56 .91 80 2120 7560 8 16 132 140 0 1509 177 1332 1.242 1487 1310 .805 1.24 .313 .31 .313
8 8400 18699 261 237 8139 18462 8462 18786 268 236 8201 18549 0 0 3334 7124 83 70 100 100 100 100 26601 26750 .441 2.268 2.262 2.335 2.301 1.264 52 319 2.267 .98 90 2260 7560 7 16 145 154 0 14840 188 14652 1.8 14910 14721 .555 1.795 .848 .844 .848
9 1752 5157 252 217 1500 4940 1772 5349 258 219 1520 5132 0 0 543 1244 71 68 100 100 100 100 6440 6652 .304 3.293 3.376 3.421 3.449 1.307 52 266 3.279 .95 80 2410 7560 8 16 161 169 0 4093 172 3921 2.614 4245 4073 .383 2.68 1.386 1.422 1.386
10 666 837 252 206 414 631 608 801 262 208 356 595 0 0 227 272 77 68 98 98 86 96 1045 951 .656 1.524 1.671 1.574 1.562 1.819 52 246 1.514 .85 80 2560 7560 8 16 176 184 0 664 163 501 1.21 636 472 .827 1.326 .275 .408 .275
11 2419 3289 250 232 2169 3057 2479 3280 254 231 2229 3048 0 0 752 982 74 64 100 100 100 100 5226 5277 .71 1.409 1.367 1.429 1.399 1.345 52 256 1.417 .96 80 2700 7560 8 16 190 198 0 2610 184 2426 1.119 2603 2419 .894 1.085 .162 .118 .162
12 2137 2477 251 216 1886 2261 2162 2583 256 226 1911 2367 0 0 554 653 74 86 100 100 98 100 4147 4278 .834 1.199 1.239 1.207 1.208 1.494 52 259 1.199 .93 80 2850 7560 8 16 205 213 0 1966 171 1794 .951 2050 1879 1.051 .983 -.072 -.025 -.072
13 1456 1728 268 212 1188 1516 1584 1804 272 227 1316 1592 0 0 457 490 83 98 100 100 96 100 2704 2908 .784 1.276 1.21 1.357 1.288 1.526 32 213 1.191 .92 70 2990 7550 7 14 219 226 0 1371 168 1203 1.013 1432 1263 .987 .96 .018 -.059 .018
14 746 606 260 213 486 393 767 633 272 222 507 420 0 0 234 162 86 70 94 98 90 92 879 927 1.237 .809 .828 .805 .745 1.819 52 288 .765 .83 80 3140 7560 8 16 234 242 0 481 169 312 .642 502 333 1.558 .657 -.64 -.605 -.64
15 7205 13809 263 205 6942 13604 7410 14679 276 216 7147 14474 0 0 2072 4306 83 69 100 100 100 100 20546 21621 .51 1.96 2.025 1.944 1.973 1.386 52 317 2.053 .96 90 3290 7560 7 16 248 257 0 10960 163 10797 1.555 11650 11487 .643 1.607 .637 .685 .637
16 2678 4544 256 212 2422 4332 2916 4709 265 216 2660 4497 0 0 824 1088 80 70 100 100 100 100 6754 7157 .559 1.789 1.691 1.904 1.774 1.522 52 305 1.698 .94 90 3430 7550 6 15 262 271 0 3606 168 3438 1.42 3737 3569 .704 1.342 .505 .424 .505
17 609 573 254 212 355 361 621 581 263 217 367 369 0 0 168 136 78 71 90 100 90 90 716 736 .983 1.017 1.005 1.066 .914 2.714 32 224 1.004 .66 70 3580 7550 7 14 278 285 0 455 168 287 .807 461 293 1.239 .798 -.309 -.326 -.309
18 596 395 266 191 330 204 587 399 272 198 321 208 0 0 154 145 80 72 96 81 90 71 534 529 1.618 .618 .648 .577 .705 2.598 32 164 .596 .56 60 3730 7560 9 15 294 300 0 313 152 162 .491 317 165 2.038 .514 -1.027 -.959 -1.027
19 1457 1595 263 159 1194 1436 1470 1623 270 164 1207 1464 0 0 561 551 81 55 100 100 98 100 2630 2671 .831 1.203 1.213 1.279 1.265 1.521 52 281 1.166 .94 80 3870 7560 8 16 307 315 0 1266 126 1140 .955 1288 1162 1.048 .963 -.067 -.055 -.067
20 701 455 292 171 409 284 740 464 291 174 448 293 0 0 178 110 77 62 93 96 93 93 693 741 1.44 .694 .654 .719 .706 1.724 32 220 .644 .76 70 4020 7550 7 14 322 329 0 361 136 225 .551 368 233 1.815 .519 -.86 -.946 -.86

Total number of rows: 43008

Table truncated, full table size 9606 Kbytes.




Supplementary data files not provided
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