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Sample GSM39994 Query DataSets for GSM39994
Status Public on Feb 21, 2005
Title Heart 2869
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Heart 2869
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-12/36431.gif
Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.48; Parameter Scan Time = 11:25:07; Parameter PMT Volts = 550; Parameter Scan Date = 2002-12-14; Parameter Pixel Size = 10; Parameter Laser on time = 45144; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 4.73; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Radha,,Shyamsundar
Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.48; Parameter Scan Time = 11:25:07; Parameter PMT Volts = 750; Parameter Scan Date = 2002-12-14; Parameter Pixel Size = 10; Parameter Laser on time = 264139; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.11; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Radha,,Shyamsundar
 
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 GPL1826
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
1 235 617 79 121 156 496 234 623 81 140 155 502 0 0 54 207 16 86 100 96 100 92 652 657 .315 3.179 3.239 3.018 3.37 1.768 52 227 3.92 .82 80 1560 8560 84 92 84 92 -100 780 153 627 4.02 788 635 .249 4.095 2.034 2.007
2 218 476 79 114 139 362 222 485 81 127 143 371 0 0 55 175 16 75 96 92 96 86 501 514 .384 2.604 2.594 2.367 2.752 2.235 52 263 3.619 .73 80 1690 8550 83 91 97 105 -100 602 144 458 3.293 613 469 .304 3.28 1.714 1.719
3 294 392 84 132 210 260 299 408 85 142 215 276 0 0 77 166 17 75 96 84 96 78 470 491 .808 1.238 1.284 1.075 1.367 2.467 32 170 1.844 .7 60 1840 8540 83 89 113 119 -100 496 167 329 1.565 516 349 .639 1.623 .699 .647
4 222 513 84 124 138 389 218 496 87 137 134 372 0 0 52 158 20 64 100 100 100 96 527 506 .355 2.819 2.776 2.748 3.06 1.655 32 159 3.511 .74 60 2000 8550 84 90 129 135 -100 649 157 492 3.564 627 470 .281 3.51 1.812 1.834
5 299 825 82 120 217 705 299 811 84 132 217 691 0 0 75 221 17 58 98 100 98 100 922 908 .308 3.249 3.184 3.429 3.267 1.783 52 269 3.559 .85 80 2130 8550 83 91 141 149 -100 1043 152 891 4.108 1025 874 .243 4.026 2.009 2.038
6 216 593 85 133 131 460 225 587 88 159 140 454 0 0 50 211 21 99 96 96 94 88 591 594 .285 3.511 3.243 3.379 3.545 1.703 52 286 4.316 .81 80 2280 8550 83 91 156 164 -100 750 168 582 4.44 742 574 .225 4.1 2.036 2.151
7 305 765 87 146 218 619 294 672 90 162 207 526 0 0 168 430 21 84 98 100 98 100 837 733 .352 2.839 2.541 2.903 2.825 1.573 52 263 2.921 .89 80 2430 8550 83 91 171 179 -100 967 185 783 3.59 850 665 .279 3.213 1.684 1.844
8 197 471 85 141 112 330 190 460 96 192 105 319 0 0 51 147 99 374 57 31 5 0 442 424 .339 2.946 3.038 2.939 3.124 1.926 80 376 3.773 .79 100 2570 8550 82 92 184 194 -100 596 178 417 3.726 582 403 .268 3.841 1.942 1.897
9 217 482 85 134 132 348 208 466 86 145 123 332 0 0 38 130 17 69 100 100 100 96 480 455 .379 2.636 2.699 2.539 2.699 1.622 52 256 3.428 .77 80 2730 8540 82 90 201 209 -100 609 169 440 3.333 589 420 .3 3.413 1.771 1.737
10 217 599 83 137 134 462 216 641 92 154 133 504 0 0 57 184 34 90 96 94 84 94 596 637 .29 3.448 3.789 3.438 3.386 1.56 52 311 4.012 .82 90 2870 8550 82 91 214 223 -100 757 173 584 4.359 810 637 .229 4.792 2.26 2.124
11 362 954 79 127 283 827 391 984 82 140 312 857 0 0 127 414 18 80 96 97 93 93 1110 1169 .342 2.922 2.747 2.79 2.968 2.069 80 377 3.344 .88 100 3010 8550 82 92 228 238 -100 1206 161 1046 3.695 1244 1084 .271 3.473 1.796 1.886
12 637 782 76 119 561 663 642 738 90 231 566 619 0 0 274 391 172 1450 94 3 73 0 1224 1185 .846 1.182 1.094 1.089 1.305 1.845 52 256 1.298 .86 80 3160 8540 82 90 244 252 -100 989 150 838 1.494 933 783 .669 1.383 .468 .579
13 235 728 78 127 157 601 247 749 91 218 169 622 0 0 57 227 156 1314 59 0 0 0 758 791 .261 3.828 3.68 3.91 3.983 1.602 52 312 197.332 .1 90 3310 8550 82 91 258 267 -100 921 161 760 4.84 947 786 .207 4.654 2.218 2.275
14 241 559 81 127 160 432 244 582 83 136 163 455 0 0 42 152 16 63 100 100 100 100 592 618 .37 2.7 2.791 2.629 2.633 1.532 52 300 3.615 .78 90 3460 8540 81 90 273 282 -100 707 161 546 3.414 736 575 .293 3.53 1.819 1.771
15 334 1492 80 119 254 1373 341 1501 81 133 261 1382 0 0 70 351 13 67 98 100 98 98 1627 1643 .185 5.406 5.295 5.403 5.498 1.31 52 277 5.776 .9 90 3590 8540 81 90 286 295 0 1887 150 1736 6.835 1898 1747 .146 6.695 2.773 2.743 2.773
16 1640 2112 76 115 1564 1997 1755 2129 78 127 1679 2014 0 0 559 960 14 64 100 97 100 97 3561 3693 .783 1.277 1.2 1.117 1.315 2.123 80 389 1.374 .93 100 3740 8540 81 91 301 311 0 2670 145 2525 1.614 2692 2547 .619 1.517 .691 .601 .691
17 319 868 73 107 246 761 338 868 76 120 265 761 0 0 81 326 13 55 100 98 100 98 1007 1026 .323 3.093 2.872 2.861 3.237 2.022 52 248 3.66 .85 80 3890 8540 82 90 317 325 -100 1098 135 962 3.911 1098 962 .256 3.631 1.86 1.968
18 171 427 76 112 95 315 117 296 80 127 41 184 0 0 104 324 16 73 81 87 62 68 410 225 .302 3.316 4.488 4.512 4.442 2.244 32 160 4.547 .7 60 4020 8540 83 89 331 337 -100 540 142 398 4.193 374 233 .239 5.675 2.504 2.068
19 399 609 78 112 321 497 399 598 80 124 321 486 0 0 134 255 15 62 100 97 100 93 818 807 .646 1.548 1.514 1.508 1.597 1.822 80 424 1.733 .87 100 4180 8540 81 91 345 355 -100 770 142 628 1.958 756 615 .511 1.914 .937 .969
20 304 530 77 110 227 420 306 527 77 119 229 417 0 0 62 178 15 55 100 98 100 96 647 646 .54 1.85 1.821 1.765 1.855 1.705 52 288 2.289 .8 90 4320 8540 81 90 359 368 -100 670 139 531 2.339 666 527 .427 2.302 1.203 1.226

Total number of rows: 43104

Table truncated, full table size 9171 Kbytes.




Supplementary data files not provided

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