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Sample GSM39948 Query DataSets for GSM39948
Status Public on Feb 21, 2005
Title Liver 1267
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Liver 1267
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-07/31005.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 GPL1824
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
1 433 202 123 232 310 -30 433 199 124 241 310 -33 0 0 73 37 25 59 100 0 100 0 280 277 null null null .067 .103 2.502 52 287 11.549 .22 80 1590 7290 53 61 67 75 0 331 380 -49 null 326 null null null null null null
2 364 167 129 215 235 -48 368 160 133 223 239 -55 0 0 44 30 30 49 100 0 100 0 187 184 null null null .052 .068 1.846 32 201 5.051 .36 70 1740 7300 54 61 82 89 0 274 352 -79 null 262 null null null null null null
3 1442 392 125 224 1317 168 1529 385 128 229 1404 161 0 0 339 89 27 50 100 88 100 80 1485 1565 7.839 .128 .115 .119 .119 1.614 80 384 .13 .79 100 1880 7290 52 62 95 105 0 643 367 275 .209 631 264 4.782 .188 -2.258 -2.411 -2.258
4 3820 4248 126 207 3694 4041 3985 4383 130 213 3859 4176 0 0 883 1768 29 48 100 100 100 98 7735 8035 .914 1.094 1.082 .896 1.131 2.087 52 312 1.196 .94 90 2030 7290 52 61 110 119 0 6964 339 6625 1.793 7185 6846 .558 1.774 .843 .827 .843
5 449 1900 123 203 326 1697 456 1911 126 207 333 1708 0 0 54 256 26 45 100 100 100 100 2023 2041 .192 5.206 5.129 5.22 5.354 1.219 52 264 5.449 .94 80 2180 7290 53 61 126 134 0 3115 333 2782 8.534 3133 2800 .117 8.408 3.093 3.072 3.093
6 336 485 122 204 214 281 341 487 124 209 219 283 0 0 71 80 26 45 100 100 98 100 495 502 .762 1.313 1.292 1.348 1.355 1.593 52 286 1.336 .82 90 2330 7300 53 62 140 149 0 795 334 461 2.153 798 464 .465 2.118 1.106 1.083 1.106
7 695 3813 121 204 574 3609 692 3851 123 212 571 3647 0 0 161 512 26 48 100 100 100 100 4183 4218 .159 6.287 6.387 6.371 6.463 1.222 52 277 6.712 .88 90 2470 7290 52 61 154 163 0 6251 334 5916 10.307 6313 5979 .097 10.471 3.366 3.388 3.366
8 6239 3565 118 196 6121 3369 7519 4020 121 200 7401 3824 0 0 2507 1235 24 41 100 100 100 100 9490 11225 1.817 .55 .517 .627 .556 2.434 80 395 .518 .93 100 2620 7290 52 62 169 179 0 5844 321 5523 .902 6590 6269 1.108 .847 -.148 -.24 -.148
9 560 677 121 183 439 494 594 724 123 189 473 541 0 0 145 211 26 40 100 98 100 96 933 1014 .889 1.125 1.144 1.087 1.146 1.772 52 255 1.201 .88 80 2760 7290 53 61 184 192 0 1110 300 810 1.845 1187 887 .542 1.875 .883 .907 .883
10 234 186 123 184 111 2 222 177 124 185 99 -7 0 0 88 53 25 35 82 23 71 11 113 92 55.5 .018 null .355 .233 4.851 52 266 .192 .2 80 2910 7280 52 60 199 207 0 305 302 3 .03 290 null 33.855 null -5.081 null -5.081
11 1237 496 120 188 1117 308 1300 513 124 190 1180 325 0 0 311 110 26 40 100 96 100 95 1425 1505 3.627 .276 .275 .267 .287 1.703 80 388 .264 .9 100 3060 7290 52 62 213 223 0 813 308 505 .452 841 533 2.212 .452 -1.146 -1.147 -1.146
12 813 340 120 179 693 161 789 336 123 185 669 157 0 0 228 102 26 45 100 87 100 75 854 826 4.304 .232 .235 .218 .234 1.799 32 211 .229 .75 70 3200 7280 52 59 228 235 0 557 293 264 .381 551 257 2.626 .385 -1.393 -1.378 -1.393
13 515 509 124 178 391 331 530 498 125 180 406 320 0 0 116 98 24 38 100 100 100 98 722 726 1.181 .847 .788 .852 .846 1.678 52 285 .845 .89 80 3350 7290 53 61 243 251 0 834 292 543 1.388 816 525 .721 1.292 .473 .37 .473
14 340 172 122 175 218 -3 338 173 125 179 216 -2 0 0 56 37 24 38 100 9 100 6 215 214 null null null .106 .087 2.714 32 170 .021 .04 60 3500 7290 54 60 259 265 0 282 287 -5 null 284 null null null null null null
15 3989 1952 118 188 3871 1764 3972 1978 119 189 3854 1790 0 0 706 428 26 37 100 100 100 100 5635 5644 2.194 .456 .464 .449 .461 1.316 52 335 .446 .93 90 3640 7290 52 61 271 280 0 3200 308 2892 .747 3243 2934 1.339 .761 -.421 -.393 -.421
16 1211 1651 118 191 1093 1460 1245 1706 119 191 1127 1515 0 0 274 336 24 37 100 100 100 100 2553 2642 .749 1.336 1.344 1.345 1.303 1.229 52 332 1.314 .94 90 3790 7290 52 61 286 295 0 2707 313 2393 2.19 2797 2484 .457 2.204 1.131 1.14 1.131
17 289 149 122 184 167 -35 290 144 121 185 168 -40 0 0 43 38 24 32 100 6 100 0 132 128 null null null .104 .134 3.283 32 165 6.11 .33 60 3930 7280 53 59 302 308 0 244 302 -57 null 236 null null null null null null
18 287 180 118 183 169 -3 277 168 121 181 159 -15 0 0 34 63 24 35 100 12 100 3 166 144 null null null .179 .188 3.336 32 216 36.051 .03 70 4080 7280 52 59 316 323 0 295 300 -5 null 275 null null null null null null
19 611 233 120 179 491 54 645 239 121 179 525 60 0 0 141 36 25 37 100 71 98 31 545 585 9.093 .11 .114 .114 .129 2.016 80 409 .101 .56 100 4220 7280 51 61 329 339 0 382 293 89 .18 392 98 5.546 .187 -2.472 -2.416 -2.472
20 301 182 118 169 183 13 297 172 121 172 179 3 0 0 44 37 24 35 100 28 100 9 196 182 14.077 .071 .017 .174 .229 2.811 32 214 .017 .03 70 4370 7280 52 59 345 352 0 298 277 21 .116 282 5 8.587 .027 -3.102 -5.186 -3.102

Total number of rows: 43008

Table truncated, full table size 9319 Kbytes.




Supplementary data files not provided
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