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Sample GSM39989 Query DataSets for GSM39989
Status Public on Feb 21, 2005
Title Muscle, right calf 0315
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Muscle, right calf 0315
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-04/15161.gif
Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-03/14254.gif
Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-04/16071.gif
Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-03/14621.gif
Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-05/17018.gif
Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-03/14265.gif
Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-03/14631.gif
Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-04/15157.gif
Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-03/14259.gif
Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-04/15158.gif
Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-03/14624.gif
Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-04/16075.gif
Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-02/13729.gif
Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-03/14628.gif
Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-05/16371.gif
Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-07/18361.gif
Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-04/16010.gif
Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-05/16397.gif
Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-04/16011.gif
Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-05/16389.gif
Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-04/16012.gif
Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-06/17378.gif
Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-03/14875.gif
Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-03/14876.gif
Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-03/14877.gif
Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-03/14878.gif
Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-04/16015.gif
Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-03/14250.gif
Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-05/17020.gif
^SAMPLE: GSM39962
^SAMPLE: GSM39963
^SAMPLE: GSM39964
^SAMPLE: GSM39965
^SAMPLE: GSM39966
^SAMPLE: GSM39967
^SAMPLE: GSM39968
^SAMPLE: GSM39969
^SAMPLE: GSM39970
^SAMPLE: GSM39971
^SAMPLE: GSM39972
^SAMPLE: GSM39973
^SAMPLE: GSM39974
^SAMPLE: GSM39975
^SAMPLE: GSM39976
^SAMPLE: GSM39977
^SAMPLE: GSM39978
^SAMPLE: GSM39979
^SAMPLE: GSM39980
^SAMPLE: GSM39981
^SAMPLE: GSM39982
^SAMPLE: GSM39983
^SAMPLE: GSM39984
^SAMPLE: GSM39985
^SAMPLE: GSM39986
^SAMPLE: GSM39987
^SAMPLE: GSM39988
^SAMPLE: GSM39989
 
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
1 464 481 206 244 258 237 462 471 214 249 256 227 0 0 105 150 60 54 96 90 86 82 495 483 1.089 .919 .887 .811 .843 2.12 52 279 1.119 .72 90 1000 9870 66 75 55 64 0 325 165 160 .621 318 153 1.611 .599 -.688 -.739 -.688
2 239 263 198 238 41 25 218 241 204 243 20 3 0 0 90 99 66 59 31 26 10 11 66 23 1.64 .61 .15 .831 .895 5.131 80 353 .855 .56 100 1090 9860 65 75 64 74 -50 178 161 17 .412 163 2 2.427 .101 -3.303 -1.279
3 1984 3553 180 229 1804 3324 1847 3336 190 236 1667 3107 0 0 623 1226 62 64 100 100 100 100 5128 4774 .543 1.843 1.864 1.817 1.806 1.211 80 240 1.9 .98 100 1270 9880 67 77 82 92 0 2401 155 2246 1.245 2254 2099 .803 1.259 .316 .333 .316
4 219 276 164 224 55 52 196 245 170 229 32 21 0 0 100 114 44 55 40 30 18 18 107 53 1.058 .945 .656 .876 1.069 4.484 80 274 1.559 .49 100 1370 9860 65 75 92 102 -50 186 151 35 .639 166 14 1.565 .443 -1.173 -.647
5 408 353 176 230 232 123 408 332 180 232 232 102 0 0 72 106 55 54 100 75 98 44 355 334 1.886 .53 .44 .408 .508 3.14 52 272 .602 .54 90 1530 9870 66 75 108 117 0 239 155 83 .358 224 69 2.792 .297 -1.481 -1.751 -1.481
6 317 393 177 225 140 168 303 385 180 227 126 160 0 0 109 114 45 61 81 81 68 62 308 286 .833 1.2 1.27 1.371 1.226 2.929 32 112 1.326 .61 60 1670 9880 69 75 124 130 0 266 152 114 .811 260 108 1.233 .858 -.303 -.221 -.303
7 323 321 185 232 138 89 321 307 207 258 136 75 0 0 157 116 97 106 52 45 38 17 227 211 1.551 .645 .551 .725 .757 2.587 80 326 .766 .68 100 1770 9850 64 74 132 142 -50 217 157 60 .436 207 51 2.295 .373 -1.424 -1.198
8 413 620 178 215 235 405 423 710 223 274 245 495 0 0 191 272 132 191 63 67 47 63 640 740 .58 1.723 2.02 1.591 1.617 2.46 80 327 1.668 .87 100 1910 9850 64 74 146 156 -50 419 145 274 1.164 480 334 .859 1.365 .449 .22
9 374 288 150 124 224 164 335 259 167 158 185 135 0 0 137 107 83 130 87 59 53 21 388 320 1.366 .732 .73 .645 .768 2.804 32 148 .684 .75 60 2060 9860 67 73 163 169 0 195 84 111 .495 175 91 2.021 .493 -1.015 -1.02 -1.015
10 274 238 142 111 132 127 269 223 147 112 127 112 0 0 57 81 38 33 94 90 84 78 259 239 1.039 .962 .882 .871 .965 2.232 52 273 .999 .65 90 2190 9850 64 73 174 183 0 161 75 86 .65 151 76 1.538 .596 -.621 -.747 -.621
11 970 268 144 114 826 154 997 258 150 117 853 144 0 0 274 89 39 35 100 93 100 82 980 997 5.364 .186 .169 .177 .185 1.659 80 270 .18 .8 100 2330 9870 66 76 188 198 0 181 77 104 .126 174 97 7.938 .114 -2.989 -3.132 -2.989
12 333 440 152 121 181 319 331 425 155 127 179 304 0 0 95 174 39 42 92 94 82 88 500 483 .567 1.762 1.698 1.696 1.848 2.073 52 201 1.946 .83 80 2470 9850 65 73 203 211 0 297 82 216 1.191 287 205 .84 1.148 .252 .199 .252
13 334 382 149 125 185 257 337 371 156 129 188 246 0 0 77 93 44 42 96 98 92 98 442 434 .72 1.389 1.309 1.448 1.335 1.832 52 228 1.421 .8 90 2600 9870 66 75 215 224 0 258 84 174 .939 251 166 1.065 .884 -.091 -.178 -.091
14 371 417 154 162 217 255 363 407 161 175 209 245 0 0 76 90 46 68 100 100 100 82 472 454 .851 1.175 1.172 1.165 1.108 1.559 52 266 1.227 .78 90 2740 9860 65 74 229 238 0 282 109 172 .794 275 166 1.259 .792 -.333 -.336 -.333
15 414 768 166 211 248 557 414 701 175 218 248 490 0 0 117 262 43 60 100 100 93 100 805 738 .445 2.246 1.976 2.227 2.143 1.691 32 170 2.422 .82 70 2880 9850 65 72 244 251 0 519 143 376 1.518 474 331 .659 1.335 .602 .417 .602
16 1384 2694 166 220 1218 2474 1398 2697 173 232 1232 2477 0 0 205 349 48 57 100 100 100 100 3692 3709 .492 2.031 2.011 2.034 2.072 1.21 80 275 2.061 .96 100 3010 9860 65 75 256 266 0 1820 149 1672 1.372 1822 1674 .729 1.358 .457 .442 .457
17 442 606 166 218 276 388 433 570 170 223 267 352 0 0 122 217 44 56 98 98 96 97 664 619 .711 1.406 1.318 1.355 1.372 1.585 80 246 1.666 .84 100 3140 9860 65 75 269 279 0 409 147 262 .95 385 238 1.053 .891 -.074 -.167 -.074
18 357 338 173 221 184 117 352 328 176 225 179 107 0 0 74 87 44 58 100 77 92 42 301 286 1.573 .636 .598 .547 .61 2.51 80 261 .764 .48 100 3280 9860 65 75 283 293 0 228 149 79 .43 222 72 2.328 .404 -1.219 -1.308 -1.219
19 320 4286 176 220 144 4066 321 4466 181 227 145 4246 0 0 74 1081 47 66 92 100 76 100 4210 4391 .035 28.236 29.283 28.894 29.053 1.577 80 263 29.415 .78 100 3420 9860 65 75 297 307 0 2896 149 2747 19.078 3018 2869 .052 19.786 4.254 4.306 4.254
20 916 1271 168 222 748 1049 951 1325 174 233 783 1103 0 0 216 320 47 73 100 100 100 98 1797 1886 .713 1.402 1.409 1.378 1.39 1.368 80 251 1.448 .94 100 3550 9860 65 75 310 320 0 859 150 709 .948 895 745 1.055 .952 -.078 -.071 -.078

Total number of rows: 44160

Table truncated, full table size 9784 Kbytes.




Supplementary data files not provided
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