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Sample GSM40001 Query DataSets for GSM40001
Status Public on Feb 21, 2005
Title Heart 0477
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Heart 0477
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-12/36420.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 = 30.81; Parameter Scan Time = 12:18:47; Parameter PMT Volts = 685; Parameter Scan Date = 2002-12-13; Parameter Pixel Size = 10; Parameter Laser on time = 44758; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.31; 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 = 30.81; Parameter Scan Time = 12:18:47; Parameter PMT Volts = 700; Parameter Scan Date = 2002-12-13; Parameter Pixel Size = 10; Parameter Laser on time = 263753; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.13; 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 1209 620 310 182 899 438 1172 641 315 192 862 459 0 0 189 168 57 58 100 96 100 93 1337 1321 2.053 .487 .532 .446 .48 1.519 32 190 .501 .91 70 1740 8270 63 70 54 61 0 664 195 469 .522 686 491 1.917 .57 -.939 -.811 -.939
2 1620 941 304 195 1316 746 1596 922 308 200 1292 727 0 0 588 306 61 58 100 100 100 98 2062 2019 1.764 .567 .563 .58 .555 1.306 52 290 .549 .96 90 1870 8280 63 72 66 75 0 1008 209 799 .607 987 778 1.647 .603 -.72 -.731 -.72
3 1864 1983 315 193 1549 1790 1862 1897 315 203 1547 1704 0 0 931 1133 62 64 98 96 96 96 3339 3251 .865 1.156 1.101 1.137 1.141 1.328 52 275 1.182 .98 80 2030 8270 63 71 83 91 0 2123 207 1917 1.237 2031 1825 .808 1.179 .307 .238 .307
4 1151 371 324 206 827 165 1193 379 325 214 869 173 0 0 218 68 66 59 100 93 100 71 992 1042 5.012 .2 .199 .189 .203 1.768 32 198 .175 .7 70 2170 8270 63 70 97 104 0 397 221 177 .214 406 185 4.681 .213 -2.227 -2.23 -2.227
5 2048 4631 320 200 1728 4431 2127 4577 319 214 1807 4377 0 0 415 1270 62 80 100 100 100 100 6159 6184 .39 2.564 2.422 2.531 2.522 1.195 52 313 2.608 .98 90 2320 8270 62 71 111 120 0 4959 214 4745 2.746 4901 4687 .364 2.594 1.457 1.375 1.457
6 799 368 314 193 485 175 783 381 312 197 469 188 0 0 176 89 57 59 100 80 100 73 660 657 2.771 .361 .401 .323 .377 2.011 52 244 .333 .72 80 2460 8270 63 71 126 134 0 394 207 187 .386 408 201 2.588 .429 -1.372 -1.22 -1.372
7 1536 1082 323 201 1213 881 1567 1069 323 208 1244 868 0 0 431 336 61 60 100 100 100 98 2094 2112 1.377 .726 .698 .71 .728 1.265 52 254 .723 .96 80 2610 8270 63 71 141 149 0 1159 215 943 .778 1145 929 1.286 .747 -.363 -.421 -.363
8 1130 2030 322 196 808 1834 1106 2029 323 211 784 1833 0 0 265 528 59 91 100 100 100 100 2642 2617 .441 2.27 2.338 2.303 2.312 1.295 52 302 2.3 .95 90 2750 8270 62 71 154 163 0 2174 210 1964 2.43 2173 1963 .411 2.504 1.281 1.324 1.281
9 1097 871 315 198 782 673 1115 916 319 207 800 718 0 0 253 267 63 64 100 97 100 97 1455 1518 1.162 .861 .898 .827 .833 1.419 80 385 .871 .93 100 2910 8270 62 72 170 180 0 933 212 721 .922 981 769 1.085 .961 -.118 -.057 -.118
10 937 409 312 202 625 207 962 403 310 210 650 201 0 0 203 104 61 65 100 93 100 75 832 851 3.019 .331 .309 .299 .313 1.617 32 192 .327 .77 70 3050 8260 62 69 185 192 0 438 216 222 .355 432 215 2.82 .331 -1.496 -1.595 -1.496
11 2596 6069 311 204 2285 5865 2667 6086 313 218 2356 5882 0 0 432 1172 62 85 100 100 100 100 8150 8238 .39 2.567 2.497 2.568 2.571 1.133 52 302 2.571 .98 90 3190 8270 62 71 198 207 0 6499 218 6280 2.748 6517 6298 .364 2.673 1.459 1.419 1.459
12 6895 6684 315 202 6580 6482 7065 6805 322 232 6750 6603 0 0 3684 3769 96 116 100 100 100 100 13062 13353 1.015 .985 .978 .959 .991 1.272 52 268 .992 .99 80 3330 8260 62 70 213 221 0 7157 216 6941 1.055 7287 7070 .948 1.047 .077 .067 .077
13 1176 1050 316 201 860 849 1160 1079 329 222 844 878 0 0 331 355 106 125 100 100 100 92 1709 1722 1.013 .987 1.04 .958 1.002 1.331 80 364 1.011 .96 100 3490 8270 62 72 228 238 0 1124 215 909 1.057 1155 940 .946 1.114 .08 .156 .08
14 902 595 320 202 582 393 906 595 334 221 586 393 0 0 182 143 103 123 100 98 98 84 975 979 1.481 .675 .671 .671 .66 1.651 52 288 .607 .82 90 3620 8270 62 71 241 250 0 637 216 421 .723 637 421 1.383 .718 -.468 -.478 -.468
15 2420 2927 318 216 2102 2711 2306 2830 1846 1840 1988 2614 0 0 672 1045 7695 8186 0 1 0 0 4813 4602 .775 1.29 1.315 1.278 1.275 1.148 52 286 1.089 .99 90 3780 8270 62 71 257 266 -100 3134 231 2903 1.381 3030 2799 .724 1.408 .494 .466
16 10786 18240 308 206 10478 18034 11513 19243 1378 1345 11205 19037 0 0 3879 6062 6471 6883 85 93 25 78 28512 30242 .581 1.721 1.699 1.753 1.722 1.124 80 409 1.317 .96 110 3920 8270 61 72 270 281 0 19531 221 19311 1.843 20605 20385 .543 1.819 .882 .863 .882
17 2226 2434 298 210 1928 2224 2318 2410 428 350 2020 2200 0 0 685 863 1012 1075 86 90 50 53 4152 4220 .867 1.154 1.089 1.157 1.167 1.257 52 252 1.176 .97 80 4070 8270 63 71 287 295 0 2606 225 2381 1.235 2581 2356 .81 1.166 .305 .222 .305
18 549 397 295 207 254 190 328 218 303 225 33 11 0 0 616 533 70 99 38 19 25 19 444 44 1.337 .748 .333 .864 .844 3.421 52 252 .875 .94 80 4230 8260 62 70 303 311 -50 425 222 203 .801 233 12 1.248 .357 -1.486 -.32
19 5519 5599 313 210 5206 5389 5904 6144 325 236 5591 5934 0 0 1300 1469 82 109 100 100 100 100 10595 11525 .966 1.035 1.061 1.026 1.04 1.156 80 420 1.042 .99 110 4370 8270 61 72 315 326 0 5995 225 5770 1.108 6579 6354 .902 1.136 .149 .185 .149
20 3480 2786 310 197 3170 2589 3626 3021 317 208 3316 2824 0 0 907 798 79 71 100 100 100 100 5759 6140 1.224 .817 .852 .809 .81 1.166 52 298 .827 .98 90 4510 8260 61 70 330 339 0 2983 211 2772 .875 3235 3024 1.143 .912 -.193 -.133 -.193

Total number of rows: 43104

Table truncated, full table size 9613 Kbytes.




Supplementary data files not provided
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