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Sample GSM39975 Query DataSets for GSM39975
Status Public on Feb 21, 2005
Title Heart 0024
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Heart 0024
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://jdemeter-smd.stanford.edu:8000/MicroArray/gifs/2001-05/16371.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 GPL1825
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
1 310 176 141 100 169 76 293 158 143 104 152 58 0 0 94 75 38 39 95 66 87 36 245 210 2.224 .45 .382 .423 .48 2.308 80 406 .482 .62 100 1050 9800 83 93 72 82 0 178 101 77 .454 160 59 2.201 .385 -1.138 -1.375 -1.138
2 326 247 133 103 193 144 309 237 134 106 176 134 0 0 113 133 34 38 96 71 87 71 337 310 1.34 .746 .761 .661 .959 2.878 32 134 .947 .68 60 1200 9780 83 89 89 95 0 249 104 145 .754 239 135 1.327 .769 -.408 -.379 -.408
3 1529 841 140 92 1389 749 1583 833 141 99 1443 741 0 0 540 324 32 37 98 98 98 96 2138 2184 1.854 .539 .514 .519 .558 1.516 80 285 .531 .94 100 1320 9800 83 93 99 109 0 849 93 757 .545 841 748 1.836 .519 -.877 -.947 -.877
4 384 319 144 101 240 218 416 294 144 107 272 193 0 0 129 130 31 41 100 100 91 91 458 465 1.101 .908 .71 .946 .8 1.953 12 85 .889 .77 50 1460 9800 85 90 115 120 0 322 102 220 .918 297 195 1.09 .717 -.124 -.481 -.124
5 439 1648 140 90 299 1558 420 1587 142 95 280 1497 0 0 90 492 30 37 100 100 100 100 1857 1777 .192 5.211 5.346 5.18 5.112 1.451 80 328 5.815 .88 110 1600 9800 82 93 126 137 0 1665 91 1574 5.263 1603 1512 .19 5.4 2.396 2.433 2.396
6 237 171 139 96 98 75 241 150 144 98 102 54 0 0 78 67 29 33 84 71 65 40 173 156 1.307 .765 .529 .735 .866 2.1 32 120 .871 .59 60 1730 9800 85 91 142 148 0 173 97 76 .773 152 55 1.294 .535 -.371 -.903 -.371
7 375 160 139 100 236 60 365 150 146 104 226 50 0 0 90 48 42 41 100 65 100 26 296 276 3.933 .254 .221 .249 .24 2.029 52 254 .253 .51 90 1880 9790 82 91 155 164 0 162 101 61 .257 152 51 3.894 .223 -1.961 -2.162 -1.961
8 536 377 142 105 394 272 544 386 151 110 402 281 0 0 139 123 44 46 97 96 96 92 666 683 1.449 .69 .699 .673 .694 1.515 80 294 .705 .86 110 2010 9800 82 93 167 178 0 381 106 275 .697 390 284 1.434 .706 -.52 -.502 -.52
9 300 121 139 106 161 15 277 123 143 107 138 17 0 0 83 39 32 37 100 34 96 3 176 155 10.733 .093 .123 .202 .263 2.162 32 132 .141 .27 60 2140 9770 82 88 183 189 0 122 107 15 .094 124 17 10.626 .124 -3.41 -3.007 -3.41
10 285 216 148 105 137 111 274 189 152 111 126 84 0 0 66 102 37 43 96 78 82 48 248 210 1.234 .81 .667 .771 .988 2.281 52 200 1.051 .56 80 2280 9770 81 89 196 204 -100 218 106 112 .818 191 85 1.222 .673 -.57 -.289
11 1077 208 150 110 927 98 1140 172 155 114 990 62 0 0 320 118 38 40 100 65 100 45 1025 1052 9.459 .106 .063 .095 .089 2.11 80 307 .122 .64 100 2410 9780 81 91 208 218 0 210 111 99 .107 174 63 9.365 .063 -3.227 -3.983 -3.227
12 481 845 155 107 326 738 457 841 158 111 302 734 0 0 152 352 36 42 100 100 100 100 1064 1036 .442 2.264 2.43 2.202 2.374 1.657 32 179 2.441 .89 70 2550 9760 80 87 223 230 -100 854 108 745 2.287 849 741 .437 2.455 1.296 1.193
13 343 365 154 109 189 256 329 322 157 117 175 213 0 0 73 177 34 40 100 98 96 94 445 388 .738 1.354 1.217 1.18 1.274 1.911 52 255 1.658 .73 90 2690 9780 81 90 236 245 -100 369 110 259 1.368 325 215 .731 1.229 .298 .452
14 416 515 152 112 264 403 406 427 156 115 254 315 0 0 112 307 43 41 100 100 100 90 667 569 .655 1.527 1.24 1.229 1.287 1.827 52 258 1.879 .81 90 2820 9770 80 89 249 258 -100 520 113 407 1.542 431 318 .649 1.253 .325 .625
15 351 567 153 109 198 458 337 500 155 115 184 391 0 0 111 333 44 45 96 92 80 92 656 575 .432 2.313 2.125 1.886 2.264 2.204 52 212 2.672 .87 80 2960 9780 82 90 264 272 -100 573 110 463 2.336 505 395 .428 2.146 1.102 1.224
16 927 3899 158 118 769 3781 958 4045 158 121 800 3927 0 0 172 811 33 45 100 100 100 100 4550 4727 .203 4.917 4.909 4.92 4.973 1.258 80 317 5.153 .95 110 3100 9780 80 91 276 287 0 3938 119 3819 4.966 4086 3967 .201 4.958 2.312 2.31 2.312
17 403 236 160 118 243 118 401 229 165 122 241 111 0 0 79 64 35 43 100 84 98 65 361 352 2.059 .486 .461 .428 .448 2.219 52 177 .476 .6 80 3230 9770 81 89 291 299 0 238 119 119 .491 231 112 2.039 .465 -1.028 -1.104 -1.028
18 349 119 162 116 187 3 357 115 166 120 195 -1 0 0 75 40 51 45 97 16 90 1 190 194 62.333 .016 null .175 .173 3.142 80 263 -1 -1 100 3360 9770 80 90 303 313 0 120 117 3 .016 116 null 61.71 null -5.947 null -5.947
19 316 2023 158 123 158 1900 321 2044 240 200 163 1921 0 0 72 450 490 471 0 100 0 96 2058 2084 .083 12.025 11.785 12.858 12.407 1.592 80 244 11.699 .85 100 3490 9780 81 91 316 326 0 2043 124 1919 12.147 2065 1940 .082 11.904 3.603 3.573 3.603
20 913 490 154 124 759 366 917 435 154 128 763 311 0 0 258 220 33 43 100 98 100 96 1125 1074 2.074 .482 .408 .434 .442 1.495 80 277 .513 .89 100 3630 9770 80 90 330 340 0 495 125 370 .487 439 314 2.053 .412 -1.038 -1.28 -1.038

Total number of rows: 44160

Table truncated, full table size 9549 Kbytes.




Supplementary data files not provided

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