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Sample GSM40009 Query DataSets for GSM40009
Status Public on Feb 21, 2005
Title RNA_DNA CRG_1
Sample type mixed
 
Channel 1
Source name Cy3 - Normal female genomic DNA
Organism Homo sapiens
Extracted molecule genomic DNA
 
Channel 2
Source name Cy5 - Common reference, CRG
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Absolute transcript levels, RNA/DNA hybridizations
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-12/22925.gif
 
Submission date Jan 26, 2005
Last update date Jun 17, 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 GPL1827
Series (2)
GSE2193 Normal_human_tissues
GSE2194 Normal_human_tissues_genomic_controls

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
1 618 870 148 102 470 768 614 899 156 110 466 797 0 0 157 323 69 50 100 100 96 100 1238 1263 .612 1.634 1.71 1.578 1.658 1.537 80 477 1.796 .84 110 1830 9200 42 53 45 56 0 806 94 711 1.513 832 738 .661 1.584 .597 .663
2 749 199 154 107 595 92 751 194 158 116 597 87 0 0 142 58 34 57 100 71 100 32 687 684 6.467 .155 .146 .141 .144 1.986 80 328 .121 .51 100 1980 9190 42 52 61 71 0 184 99 85 .143 180 81 6.985 .135 -2.804 -2.89
3 481 2547 153 110 328 2437 493 2651 157 126 340 2541 0 0 135 669 36 86 100 100 95 100 2765 2881 .135 7.43 7.474 7.998 7.362 1.557 80 335 7.641 .88 100 2110 9200 43 53 74 84 0 2358 102 2256 6.88 2455 2353 .145 6.92 2.782 2.791
4 534 5577 161 119 373 5458 548 5722 165 131 387 5603 0 0 167 1857 38 76 100 100 97 100 5831 5990 .068 14.633 14.478 15.674 14.324 1.59 80 375 15.34 .89 100 2260 9200 43 53 89 99 0 5164 110 5054 13.549 5298 5188 .074 13.406 3.76 3.745
5 620 542 159 106 461 436 631 543 162 111 472 437 0 0 168 189 33 44 100 100 98 96 897 909 1.057 .946 .926 .925 .895 1.72 80 362 .988 .88 100 2410 9200 43 53 104 114 0 502 98 404 .876 503 405 1.142 .857 -.191 -.222
6 433 228 146 96 287 132 443 230 149 101 297 134 0 0 103 89 31 39 98 83 97 68 419 431 2.174 .46 .451 .385 .413 2.212 80 367 .432 .63 100 2570 9200 43 53 120 130 0 211 89 122 .426 213 124 2.348 .418 -1.232 -1.259
7 450 1035 146 106 304 929 450 1046 149 108 304 940 0 0 91 220 32 43 100 100 100 100 1233 1244 .327 3.056 3.092 3.123 2.959 1.43 80 311 3.301 .89 100 2700 9200 43 53 133 143 0 958 98 860 2.83 969 870 .353 2.863 1.501 1.518
8 1043 10820 155 105 888 10715 1151 12338 157 108 996 12233 0 0 438 5344 33 42 99 100 99 100 11603 13229 .083 12.066 12.282 12.049 12.505 1.896 120 408 13.08 .93 120 2850 9200 42 54 147 159 0 10019 97 9921 11.173 11424 11327 .09 11.372 3.482 3.507
9 747 447 162 96 585 351 779 458 161 100 617 362 0 0 271 140 35 38 98 100 97 97 936 979 1.667 .6 .587 .64 .564 1.898 80 322 .542 .86 100 2990 9200 43 53 162 172 0 414 89 325 .556 424 335 1.8 .543 -.848 -.88
10 690 178 160 89 530 89 729 176 160 95 569 87 0 0 128 58 37 37 100 80 100 61 619 656 5.955 .168 .153 .167 .188 1.947 52 291 .144 .56 90 3140 9190 42 51 177 186 0 165 82 82 .155 163 81 6.431 .142 -2.685 -2.82
11 1542 2051 156 91 1386 1960 1610 2129 159 96 1454 2038 0 0 542 612 36 40 100 100 100 100 3346 3492 .707 1.414 1.402 1.514 1.404 1.672 80 354 1.406 .92 100 3290 9200 43 53 192 202 0 1899 84 1815 1.309 1971 1887 .764 1.298 .389 .376
12 533 1306 156 97 377 1209 505 1160 159 103 349 1063 0 0 178 544 34 42 100 100 96 100 1586 1412 .312 3.207 3.046 3.392 2.912 1.775 52 314 3.551 .86 90 3430 9190 42 51 206 215 0 1209 90 1119 2.969 1074 984 .337 2.82 1.57 1.496
13 875 521 158 94 717 427 857 514 162 100 699 420 0 0 405 216 33 38 100 100 100 100 1144 1119 1.679 .596 .601 .62 .606 1.972 32 204 .509 .8 70 3570 9200 44 51 221 228 0 482 87 395 .551 476 389 1.813 .556 -.859 -.846
14 541 217 161 87 380 130 531 225 162 93 370 138 0 0 185 91 35 36 96 84 96 68 510 508 2.923 .342 .373 .308 .31 2.238 32 158 .319 .72 60 3730 9190 44 50 238 244 0 201 81 120 .317 208 128 3.157 .345 -1.659 -1.534
15 2755 8233 151 94 2604 8139 2800 8436 155 100 2649 8342 0 0 1111 2613 33 42 100 100 100 100 10743 10991 .32 3.126 3.149 3.417 3.015 1.663 80 391 3.176 .92 100 3870 9200 43 53 250 260 0 7623 87 7536 2.894 7811 7724 .346 2.916 1.533 1.544
16 1009 1736 151 93 858 1643 1002 1794 152 97 851 1701 0 0 349 366 30 41 100 100 100 100 2501 2552 .522 1.915 1.999 2.129 1.924 1.69 80 364 1.865 .91 100 4020 9200 43 53 265 275 0 1607 86 1521 1.773 1661 1575 .564 1.851 .826 .888
17 603 126 149 89 454 37 583 119 152 94 434 30 0 0 157 54 32 34 100 42 100 19 491 464 12.27 .081 .069 .094 .1 2.273 52 245 .074 .37 80 4160 9190 43 51 280 288 0 117 82 34 .075 110 28 13.252 .064 -3.728 -3.966
18 614 144 158 87 456 57 602 149 160 92 444 62 0 0 112 46 33 37 100 68 100 34 513 506 8 .125 .14 .13 .154 2.153 32 206 .101 .41 70 4310 9190 43 50 295 302 0 133 81 53 .116 138 57 8.64 .129 -3.111 -2.951
19 746 1075 159 94 587 981 770 1088 160 101 611 994 0 0 162 271 35 41 100 100 100 100 1568 1605 .598 1.671 1.627 1.712 1.739 1.665 80 441 1.726 .88 110 4460 9200 42 53 308 319 0 995 87 908 1.547 1007 920 .646 1.506 .63 .591
20 513 191 162 99 351 92 528 180 162 102 366 81 0 0 109 67 35 42 100 75 100 46 443 447 3.815 .262 .221 .214 .218 2.355 32 204 .272 .59 70 4600 9190 43 50 324 331 0 177 92 85 .243 167 75 4.12 .205 -2.043 -2.287

Total number of rows: 43008

Table truncated, full table size 9152 Kbytes.




Supplementary data files not provided

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