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Sample GSM39905 Query DataSets for GSM39905
Status Public on Feb 21, 2005
Title Brain, temporal cortex 2273
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Brain, temporal cortex 2273
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-03/26951.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
1 162 95 78 60 84 35 157 86 79 62 79 26 0 0 40 29 19 15 98 71 90 42 119 105 2.4 .417 .329 .347 .286 2.728 52 304 .311 .46 80 1270 8120 36 44 43 51 0 88 56 32 .386 80 24 2.592 .305 -1.374 -1.714 -1.374
2 158 105 79 59 79 46 153 103 83 61 74 44 0 0 39 35 28 23 92 71 75 46 125 118 1.717 .582 .595 .606 .629 2.311 52 261 .832 .64 80 1430 8120 36 44 59 67 0 97 55 43 .539 95 41 1.855 .551 -.891 -.861 -.891
3 568 273 79 64 489 209 553 266 81 64 474 202 0 0 185 82 19 17 100 100 100 100 698 676 2.34 .427 .426 .425 .437 1.522 52 242 .39 .87 80 1560 8120 36 44 72 80 0 253 59 194 .396 246 187 2.527 .395 -1.337 -1.342 -1.337
4 1516 2818 78 61 1438 2757 1530 2763 81 62 1452 2702 0 0 906 1750 19 14 100 100 100 100 4195 4154 .522 1.917 1.861 1.937 1.932 1.503 52 343 1.993 .96 90 1700 8110 34 43 85 94 0 2609 56 2553 1.775 2558 2502 .563 1.723 .828 .785 .828
5 222 340 80 61 142 279 217 352 82 63 137 291 0 0 53 109 18 14 100 100 98 100 421 428 .509 1.965 2.124 1.9 1.991 1.471 52 351 2.13 .88 90 1860 8120 35 44 101 110 0 315 56 258 1.819 326 269 .55 1.967 .863 .976 .863
6 153 143 81 64 72 79 157 139 83 64 76 75 0 0 32 28 17 12 93 100 84 100 151 151 .911 1.097 .987 1.097 .97 1.854 32 207 .907 .64 70 2000 8120 36 43 116 123 0 132 59 73 1.016 129 69 .984 .914 .023 -.13 .023
7 286 504 83 64 203 440 293 520 87 65 210 456 0 0 82 161 22 15 100 100 98 100 643 666 .461 2.167 2.171 2.197 2.191 1.422 52 256 2.187 .92 80 2140 8120 36 44 130 138 0 467 59 407 2.007 481 422 .498 2.011 1.005 1.008 1.005
8 2048 1987 84 64 1964 1923 1729 1907 91 68 1645 1843 0 0 1239 1181 39 18 100 100 100 100 3887 3488 1.021 .979 1.12 .989 .988 1.752 52 343 .954 .94 90 2280 8110 34 43 143 152 0 1840 59 1781 .907 1766 1706 1.103 1.037 -.141 .053 -.141
9 494 382 83 63 411 319 532 404 87 66 449 341 0 0 153 132 38 15 98 100 96 100 730 790 1.288 .776 .759 .775 .793 1.45 52 322 .785 .94 90 2440 8120 35 44 159 168 0 354 58 295 .719 374 316 1.391 .703 -.477 -.508 -.477
10 168 206 83 63 85 143 176 211 83 64 93 148 0 0 41 43 17 15 96 100 86 100 228 241 .594 1.682 1.591 1.87 1.586 2.086 52 254 1.643 .76 80 2580 8120 36 44 174 182 0 191 58 132 1.558 195 137 .642 1.474 .639 .559 .639
11 335 296 84 64 251 232 346 293 86 64 262 229 0 0 100 84 19 15 100 100 100 100 483 491 1.082 .924 .874 .961 .942 1.539 52 322 .902 .89 90 2720 8120 35 44 187 196 0 274 59 215 .856 271 212 1.168 .809 -.225 -.305 -.225
12 326 315 86 66 240 249 282 291 87 66 196 225 0 0 160 173 21 14 100 100 94 94 489 421 .964 1.038 1.148 .989 .979 1.925 52 262 1.058 .89 80 2880 8120 36 44 204 212 0 292 61 231 .961 269 208 1.041 1.063 -.058 .088 -.058
13 307 303 83 62 224 241 331 324 84 63 248 262 0 0 84 95 19 13 100 100 96 100 465 510 .929 1.076 1.056 1.098 1.098 1.483 52 277 1.089 .92 90 3020 8120 35 44 217 226 0 281 57 223 .996 300 243 1.004 .978 -.005 -.032 -.005
14 161 101 84 66 77 35 154 105 84 67 70 39 0 0 43 20 19 14 96 82 78 59 112 109 2.2 .455 .557 .475 .491 2.116 52 294 .332 .53 90 3160 8110 34 43 231 240 0 94 61 32 .421 97 36 2.376 .516 -1.249 -.955 -1.249
15 1458 1747 83 64 1375 1683 1573 1865 84 66 1490 1801 0 0 893 863 20 17 100 100 100 100 3058 3291 .817 1.224 1.209 1.418 1.234 1.576 80 402 1.138 .96 100 3310 8120 35 45 246 256 0 1618 59 1558 1.133 1727 1668 .882 1.119 .181 .162 .181
16 507 690 82 61 425 629 518 663 84 65 436 602 0 0 146 200 22 24 100 100 100 100 1054 1038 .676 1.48 1.381 1.516 1.476 1.428 52 309 1.466 .94 90 3450 8110 34 43 260 269 0 639 56 582 1.37 614 557 .73 1.278 .455 .354 .455
17 137 80 80 61 57 19 136 79 80 64 56 18 0 0 28 18 18 14 93 50 84 31 76 74 3 .333 .321 .333 .39 2.876 32 220 .211 .3 70 3610 8120 36 43 277 284 0 74 56 18 .309 73 17 3.24 .298 -1.696 -1.748 -1.696
18 155 74 80 61 75 13 157 71 83 63 77 10 0 0 39 16 18 15 90 40 84 12 88 87 5.769 .173 .13 .2 .222 2.658 32 220 .171 .35 70 3750 8110 35 42 291 298 0 69 56 12 .16 66 9 6.231 .12 -2.639 -3.056 -2.639
19 236 401 84 63 152 338 224 353 84 64 140 290 0 0 95 215 18 15 94 100 92 100 490 430 .45 2.224 2.071 2.272 2.174 1.676 52 307 2.372 .89 80 3890 8120 36 44 305 313 0 371 58 313 2.059 327 269 .486 1.918 1.042 .94 1.042
20 139 81 87 65 52 16 138 78 87 67 51 13 0 0 30 17 18 14 87 46 78 18 68 64 3.25 .308 .255 .323 .25 3.088 32 196 .154 .25 70 4050 8110 35 42 321 328 0 75 60 15 .285 72 12 3.51 .236 -1.811 -2.083 -1.811

Total number of rows: 43008

Table truncated, full table size 9035 Kbytes.




Supplementary data files not provided
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