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Sample GSM39907 Query DataSets for GSM39907
Status Public on Feb 21, 2005
Title Brain, frontal cortex 2273
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Brain, frontal cortex 2273
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-03/26954.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 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
1 133 115 71 73 62 42 131 105 72 75 60 32 0 0 33 57 15 25 96 57 82 36 104 92 1.476 .677 .533 .621 .753 3.317 52 301 1.409 .37 80 1250 7640 36 44 33 41 0 108 69 40 .639 99 30 1.565 .503 -.646 -.991 -.646
2 138 148 69 69 69 79 139 152 72 74 70 83 0 0 29 58 20 28 96 68 81 62 148 153 .873 1.145 1.186 .913 1.165 3.591 32 219 1.367 .48 70 1390 7640 36 43 47 54 0 140 65 75 1.08 143 78 .926 1.119 .111 .162 .111
3 320 167 71 72 249 95 315 161 73 75 244 89 0 0 126 69 18 28 97 81 96 68 344 333 2.621 .382 .365 .334 .333 2.182 80 426 .388 .7 100 1550 7650 36 46 62 72 0 158 68 90 .36 152 84 2.778 .344 -1.474 -1.539 -1.474
4 1435 1848 72 69 1363 1779 1327 1728 73 73 1255 1659 0 0 830 965 15 26 100 100 100 100 3142 2914 .766 1.305 1.322 1.332 1.144 1.686 52 320 1.278 .88 90 1690 7640 35 44 76 85 0 1743 65 1678 1.231 1630 1565 .812 1.247 .3 .319 .3
5 240 457 69 71 171 386 229 425 69 73 160 354 0 0 90 220 14 26 100 100 100 100 557 514 .443 2.257 2.213 2.197 2.04 1.76 52 312 2.58 .85 90 1840 7650 36 45 91 100 0 431 67 364 2.13 401 334 .47 2.087 1.091 1.062 1.091
6 133 438 70 71 63 367 135 452 71 73 65 381 0 0 27 140 15 26 96 100 88 100 430 446 .172 5.825 5.862 6.088 6.008 1.709 52 267 6.103 .84 80 1980 7650 37 45 106 114 0 413 67 346 5.496 426 359 .182 5.53 2.458 2.467 2.458
7 275 334 68 69 207 265 270 339 71 74 202 270 0 0 88 81 20 29 100 100 100 100 472 472 .781 1.28 1.337 1.352 1.25 1.758 52 276 1.283 .83 90 2130 7650 36 45 120 129 0 315 65 250 1.208 320 255 .828 1.261 .272 .335 .272
8 1808 1335 68 71 1740 1264 1504 1077 70 76 1436 1006 0 0 1172 790 19 28 100 100 100 100 3004 2442 1.377 .726 .701 .754 .639 2.069 52 291 .658 .84 90 2280 7640 35 44 135 144 -100 1259 67 1192 .685 1016 949 1.459 .661 -.597 -.545
9 350 218 71 70 279 148 276 221 72 74 205 151 0 0 205 94 15 28 100 88 98 80 427 356 1.885 .53 .737 .567 .533 2.842 52 253 .414 .74 80 2410 7650 37 45 149 157 0 206 66 140 .5 208 142 1.998 .695 -.999 -.525 -.999
10 186 848 73 74 113 774 188 838 74 80 115 764 0 0 54 225 16 28 100 100 92 100 887 879 .146 6.85 6.643 7.513 6.647 1.728 52 324 6.835 .86 90 2560 7640 35 44 163 172 0 800 70 730 6.462 791 721 .155 6.267 2.692 2.648 2.692
11 327 239 72 71 255 168 327 235 74 75 255 164 0 0 104 80 17 26 100 98 100 96 423 419 1.518 .659 .643 .674 .675 1.878 52 254 .624 .78 80 2710 7650 37 45 179 187 0 225 67 158 .622 222 155 1.609 .607 -.686 -.721 -.686
12 436 335 72 73 364 262 404 322 76 77 332 249 0 0 174 131 29 25 100 100 100 100 626 581 1.389 .72 .75 .726 .674 1.665 52 313 .7 .87 90 2850 7640 35 44 192 201 0 316 69 247 .679 304 235 1.473 .708 -.558 -.499 -.558
13 327 239 72 77 255 162 324 222 74 81 252 145 0 0 94 73 18 26 100 98 100 92 417 397 1.574 .635 .575 .616 .604 1.81 52 252 .646 .84 80 3000 7650 37 45 208 216 0 225 73 153 .599 209 137 1.669 .543 -.739 -.881 -.739
14 154 126 71 74 83 52 155 126 73 78 84 52 0 0 37 40 18 28 98 65 86 42 135 136 1.596 .627 .619 .54 .614 3.193 52 257 .672 .36 80 3150 7640 36 44 223 231 0 119 70 49 .591 119 49 1.692 .584 -.759 -.776 -.759
15 1572 1409 69 70 1503 1339 1544 1486 72 74 1475 1416 0 0 960 746 17 25 100 100 100 100 2842 2891 1.122 .891 .96 1.02 .919 2.006 80 329 .842 .95 100 3290 7640 35 45 236 246 0 1329 66 1263 .84 1402 1336 1.19 .906 -.251 -.143 -.251
16 397 449 68 75 329 374 394 441 71 78 326 366 0 0 121 163 15 25 100 100 100 100 703 692 .88 1.137 1.123 1.123 1.103 1.43 52 292 1.102 .88 90 3440 7640 35 44 251 260 0 424 71 353 1.072 416 345 .932 1.059 .101 .083 .101
17 129 101 73 71 56 30 133 100 75 73 60 29 0 0 33 31 18 25 84 62 65 18 86 89 1.867 .536 .483 .517 .584 4.863 32 166 .705 .2 60 3580 7650 38 44 267 273 0 95 67 28 .505 94 27 1.979 .456 -.985 -1.133 -.985
18 143 86 70 72 73 14 143 69 74 74 73 -3 0 0 26 44 16 24 100 31 96 18 87 70 5.214 .192 null .427 .623 4.621 32 202 .923 .2 70 3730 7650 37 44 281 288 0 81 68 13 .181 65 null 5.527 null -2.467 null -2.467
19 204 261 72 77 132 184 191 233 73 80 119 156 0 0 83 118 16 26 96 96 94 90 316 275 .717 1.394 1.311 1.274 1.189 2.089 52 353 1.608 .75 90 3880 7640 35 44 295 304 0 246 73 174 1.315 220 147 .76 1.237 .395 .307 .395
20 150 102 72 77 78 25 143 96 74 78 71 19 0 0 31 43 16 24 100 43 96 28 103 90 3.12 .321 .268 .403 .654 3.405 32 190 .51 .27 70 4020 7650 37 44 310 317 0 96 73 24 .302 91 18 3.307 .252 -1.726 -1.986 -1.726

Total number of rows: 43008

Table truncated, full table size 9046 Kbytes.




Supplementary data files not provided
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