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Sample GSM39979 Query DataSets for GSM39979
Status Public on Feb 21, 2005
Title Esophagus 0406
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Esophagus 0406
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://jdemeter-smd.stanford.edu:8000/MicroArray/gifs/2001-04/16011.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
1 244 234 202 246 42 -12 217 229 206 249 15 -17 0 0 84 76 43 69 40 15 26 3 30 -2 null null null 1.214 1.299 4.327 80 456 .868 .03 100 920 9220 57 67 67 77 -50 202 212 -10 null 197 null null null null null
2 414 498 214 235 200 263 412 491 211 241 198 256 0 0 71 114 45 62 100 100 100 91 463 454 .76 1.315 1.293 1.277 1.327 1.803 12 81 1.598 .68 50 1100 9260 63 68 87 92 0 429 203 227 1.134 423 221 .882 1.115 .181 .157 .181
3 1951 1842 198 234 1753 1608 1964 1863 205 242 1766 1629 0 0 615 570 52 73 100 98 100 98 3361 3395 1.09 .917 .922 .932 .911 1.351 80 201 .899 .97 100 1220 9260 61 71 97 107 0 1588 202 1386 .791 1606 1404 1.265 .795 -.339 -.331 -.339
4 224 244 197 236 27 8 198 247 212 248 1 11 0 0 92 78 85 90 15 15 11 3 35 12 3.375 .296 11 1.496 1.6 2.966 80 238 .753 .67 100 1330 9220 57 67 108 118 -50 210 203 7 .255 213 9 3.915 9.483 3.245 -1.969
5 425 522 197 231 228 291 224 295 256 297 27 64 0 0 325 383 175 216 36 40 33 36 519 91 .784 1.276 2.37 1.498 1.255 2.229 80 245 1.272 .91 100 1460 9220 57 67 121 131 -50 450 199 251 1.1 254 55 .909 2.043 1.031 .138
6 210 220 196 217 14 3 197 212 232 270 1 -5 0 0 58 63 149 194 3 0 0 0 17 -4 4.667 .214 null 1.057 1.08 3.165 80 305 1.356 .86 100 1600 9220 57 67 135 145 -50 190 187 3 .185 183 null 5.413 null null -2.437
7 639 775 199 225 440 550 622 769 215 256 423 544 0 0 181 207 76 170 98 100 98 84 990 967 .8 1.25 1.286 1.274 1.213 1.445 52 193 1.354 .82 80 1770 9250 61 69 153 161 0 668 194 474 1.078 663 469 .928 1.109 .108 .149 .108
8 1070 2409 211 237 859 2172 1102 2309 242 303 891 2072 0 0 265 601 110 216 98 100 98 98 3031 2963 .395 2.529 2.325 2.566 2.61 1.342 52 123 2.591 .92 80 1910 9250 61 69 167 175 0 2077 204 1872 2.18 1991 1786 .459 2.005 1.124 1.003 1.124
9 320 255 193 214 127 41 266 246 200 222 73 32 0 0 167 101 62 82 51 27 38 7 168 105 3.098 .323 .438 .713 .739 4.338 80 307 .617 .47 100 2010 9220 57 67 176 186 -50 220 184 35 .278 212 28 3.593 .378 -1.404 -1.845
10 368 249 185 212 183 37 368 244 200 213 183 32 0 0 68 78 61 58 96 34 78 21 220 215 4.946 .202 .175 .348 .561 3.286 32 121 .035 .03 60 2170 9220 59 65 194 200 0 215 183 32 .174 210 28 5.737 .151 -2.52 -2.73 -2.52
11 1272 14058 188 226 1084 13832 1382 15451 197 239 1194 15225 0 0 481 5136 53 73 97 98 95 98 14916 16419 .078 12.76 12.751 12.702 12.546 1.511 80 300 12.658 .97 100 2290 9220 57 67 204 214 0 12119 195 11924 11 13320 13125 .091 10.992 3.459 3.458 3.459
12 465 624 188 254 277 370 438 584 199 257 250 330 0 0 115 182 45 72 93 93 93 90 647 580 .749 1.336 1.32 1.362 1.361 1.906 32 170 1.657 .78 70 2430 9200 56 63 219 226 0 538 219 319 1.152 503 284 .868 1.138 .204 .186 .204
13 395 411 188 250 207 161 389 395 194 254 201 145 0 0 95 107 41 70 96 81 87 51 368 346 1.286 .778 .721 .77 .749 2.126 80 293 .997 .66 100 2570 9220 57 67 232 242 0 354 216 139 .67 341 125 1.491 .622 -.577 -.685 -.577
14 452 365 195 255 257 110 439 339 197 259 244 84 0 0 78 101 44 74 100 57 100 34 367 328 2.336 .428 .344 .355 .457 2.728 52 182 .54 .41 90 2700 9220 57 66 245 254 0 315 220 95 .369 292 72 2.71 .297 -1.438 -1.753 -1.438
15 288 282 197 253 91 29 257 259 201 256 60 6 0 0 109 119 42 73 60 25 42 13 120 66 3.138 .319 .1 .748 .685 3.501 80 255 1.238 .39 100 2820 9210 56 66 257 267 -50 243 218 25 .275 223 5 3.64 .086 -3.536 -1.864
16 1296 1540 192 240 1104 1300 1249 1542 196 242 1057 1302 0 0 305 373 43 68 100 100 100 100 2404 2359 .849 1.178 1.232 1.167 1.169 1.236 80 254 1.18 .95 100 2970 9220 57 67 272 282 0 1328 207 1121 1.015 1329 1122 .985 1.062 .022 .087 .022
17 394 399 183 240 211 159 385 383 185 243 202 143 0 0 80 115 41 72 97 77 93 48 370 345 1.327 .754 .708 .731 .826 2.104 80 239 1.013 .6 100 3100 9220 57 67 285 295 0 344 207 137 .65 330 123 1.539 .61 -.622 -.712 -.622
18 292 258 187 232 105 26 291 253 190 237 104 21 0 0 71 73 43 70 85 28 61 5 131 125 4.038 .248 .202 .631 .637 3.323 80 249 1.273 .17 100 3230 9210 56 66 298 308 -50 222 200 22 .213 218 18 4.685 .174 -2.522 -2.228
19 278 235 190 239 88 -4 284 235 191 244 94 -4 0 0 57 60 44 65 76 13 53 1 84 90 null null null .485 .524 4.408 80 252 .245 .04 100 3370 9210 56 66 312 322 -50 203 206 -3 null 203 null null null null null
20 937 1249 191 251 746 998 918 1273 193 258 727 1022 0 0 201 332 45 68 100 100 100 98 1744 1749 .747 1.338 1.406 1.286 1.394 1.504 80 236 1.401 .94 100 3510 9220 57 67 326 336 0 1077 216 860 1.153 1097 881 .867 1.212 .206 .277 .206

Total number of rows: 44160

Table truncated, full table size 9663 Kbytes.




Supplementary data files not provided
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