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Sample GSM39940 Query DataSets for GSM39940
Status Public on Feb 21, 2005
Title Parathyroid 1748
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Parathyroid 1748
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-11/35030.gif
 
Submission date Jan 26, 2005
Last update date Nov 22, 2005
Contact name Jonathan Pollack
E-mail(s) pollack1@stanford.edu
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 GPL1824
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
1 540 409 193 179 347 230 551 393 266 222 358 214 0 0 175 169 853 508 0 7 0 0 577 572 1.509 .663 .598 .578 .758 3.638 52 336 .792 .53 90 1620 8550 62 71 57 66 0 365 160 205 .592 351 191 1.69 .534 -.757 -.906 -.757
2 497 244 196 185 301 59 479 239 206 195 283 54 0 0 142 81 58 60 94 46 92 17 360 337 5.102 .196 .191 .277 .269 3.096 52 237 .104 .19 80 1760 8550 63 71 72 80 0 218 165 53 .175 213 48 5.714 .17 -2.514 -2.553 -2.514
3 827 2297 196 186 631 2111 875 2569 202 191 679 2383 0 0 264 714 56 49 96 100 93 100 2742 3062 .299 3.345 3.51 3.391 3.111 2.23 80 332 3.857 .81 100 1910 8560 63 73 86 96 0 2051 166 1885 2.987 2294 2128 .335 3.134 1.579 1.648 1.579
4 1902 5943 203 185 1699 5758 1867 5668 204 190 1664 5483 0 0 1182 3743 50 52 95 100 91 97 7457 7147 .295 3.389 3.295 3.031 3.429 3.465 80 344 3.916 .82 100 2050 8560 63 73 100 110 0 5306 165 5141 3.026 5061 4896 .33 2.942 1.597 1.557 1.597
5 612 310 208 188 404 122 605 315 211 194 397 127 0 0 162 83 47 58 96 75 96 57 526 524 3.311 .302 .32 .277 .314 1.969 52 257 .272 .56 80 2200 8550 63 71 116 124 0 277 168 109 .27 281 113 3.709 .286 -1.891 -1.808 -1.891
6 505 430 218 197 287 233 566 439 221 199 348 242 0 0 229 153 52 52 78 84 69 76 520 590 1.232 .812 .695 .829 .739 3.619 52 291 .621 .55 90 2350 8570 64 73 130 139 0 384 176 208 .725 392 216 1.38 .621 -.464 -.688 -.464
7 715 263 203 194 512 69 717 269 210 199 514 75 0 0 178 81 54 57 98 63 98 26 581 589 7.42 .135 .146 .15 .186 2.455 52 257 .109 .35 80 2490 8550 63 71 145 153 0 235 173 62 .12 240 67 8.311 .13 -3.055 -2.94 -3.055
8 4320 12949 210 192 4110 12757 4632 13637 214 201 4422 13445 0 0 1516 4324 60 56 95 100 95 100 16867 17867 .322 3.104 3.04 2.933 3.003 1.78 80 425 3.404 .89 100 2650 8560 63 73 160 170 0 11562 171 11390 2.771 12176 12004 .361 2.715 1.471 1.441 1.471
9 635 459 222 217 413 242 695 468 226 220 473 251 0 0 278 179 70 61 81 84 78 68 655 724 1.707 .586 .531 .616 .609 3.815 32 195 .544 .71 70 2780 8560 64 71 174 181 0 410 194 216 .523 418 224 1.911 .474 -.935 -1.078 -.935
10 426 285 221 213 205 72 382 236 223 221 161 23 0 0 187 111 57 63 76 48 59 32 277 184 2.847 .351 .143 .589 .517 3.991 52 272 .343 .37 80 2940 8550 63 71 190 198 0 254 190 64 .314 211 21 3.189 .128 -1.673 -2.971 -1.673
11 1170 1058 213 201 957 857 1227 1063 216 208 1014 862 0 0 395 258 52 57 95 100 93 100 1814 1876 1.117 .896 .85 .97 .893 2.074 80 334 .808 .86 100 3080 8560 63 73 203 213 0 945 179 765 .8 949 770 1.251 .759 -.323 -.398 -.323
12 732 640 219 198 513 442 696 583 224 204 477 385 0 0 335 309 62 56 96 92 84 84 955 862 1.161 .862 .807 .853 .894 2.398 52 235 .82 .76 80 3220 8570 65 73 218 226 0 571 177 395 .769 521 344 1.3 .721 -.378 -.473 -.378
13 629 543 218 191 411 352 646 572 224 196 428 381 0 0 205 215 56 52 94 86 90 80 763 809 1.168 .856 .89 .723 .836 2.755 52 320 .855 .78 90 3370 8560 63 72 232 241 0 485 171 314 .765 511 340 1.308 .795 -.387 -.331 -.387
14 578 281 217 210 361 71 582 271 223 213 365 61 0 0 142 119 51 56 96 53 93 21 432 426 5.085 .197 .167 .21 .221 2.27 32 151 .108 .21 60 3530 8560 65 71 250 256 0 251 188 63 .176 242 54 5.695 .149 -2.51 -2.745 -2.51
15 2519 9097 201 188 2318 8909 2690 10002 209 194 2489 9814 0 0 1501 4853 55 56 96 100 96 100 11227 12303 .26 3.843 3.943 4.019 3.694 2.5 80 386 4.305 .82 110 3660 8560 62 73 260 271 0 8122 168 7954 3.432 8930 8763 .291 3.52 1.779 1.816 1.779
16 878 5196 209 197 669 4999 933 5293 225 213 724 5096 0 0 488 2801 86 105 82 100 76 100 5668 5820 .134 7.472 7.039 7.029 7.133 3.219 52 306 8.798 .74 90 3810 8570 64 73 276 285 0 4639 176 4463 6.672 4726 4550 .15 6.285 2.738 2.652 2.738
17 607 219 226 209 381 10 606 224 270 224 380 15 0 0 105 48 127 75 100 8 91 0 391 395 38.1 .026 .039 .077 .079 2.295 12 94 21.395 .13 50 4000 8550 64 69 297 302 0 196 187 9 .023 200 13 42.672 .035 -5.415 -4.826 -5.415
18 500 211 218 199 282 12 445 202 228 201 227 3 0 0 274 77 77 60 75 18 68 9 294 230 23.5 .043 .013 .154 .177 3.914 32 195 -1 -1 70 4100 8550 63 70 306 313 0 188 178 11 .038 180 3 26.32 .012 -4.718 -6.405 -4.718
19 848 1606 215 201 633 1405 907 1732 232 209 692 1531 0 0 322 484 102 76 92 100 86 100 2038 2223 .451 2.22 2.212 2.418 2.279 2.271 80 498 2.351 .77 110 4260 8560 62 73 320 331 0 1434 179 1254 1.982 1546 1367 .505 1.975 .987 .982 .987
20 562 217 220 201 342 16 646 213 232 203 426 12 0 0 287 79 81 52 71 34 68 12 358 438 21.375 .047 .028 .218 .16 5.505 32 148 .057 .17 60 4410 8550 64 70 338 344 0 194 179 14 .042 190 11 23.94 .025 -4.581 -5.313 -4.581

Total number of rows: 43008

Table truncated, full table size 9520 Kbytes.




Supplementary data files not provided

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