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Sample GSM39961 Query DataSets for GSM39961
Status Public on Feb 21, 2005
Title Adrenal 0433
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Adrenal 0433
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://jdemeter-smd.stanford.edu:8000/MicroArray/gifs/2001-04/15161.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
1 152 173 139 167 13 6 135 168 157 176 -4 1 0 0 80 68 278 116 0 8 0 1 19 -3 2.167 .462 null .791 .821 4.074 80 363 1.037 .44 100 830 9240 75 85 58 68 -50 206 199 7 .549 200 1 1.82 null null -.864
2 145 160 130 157 15 3 137 152 165 174 7 -5 0 0 63 66 306 120 1 3 0 1 18 2 5 .2 null 1.347 1.211 4.008 80 334 .389 .86 100 960 9240 75 85 71 81 -50 190 187 4 .238 181 null 4.2 null null -2.07
3 1001 567 140 153 861 414 235 238 155 167 95 85 0 0 1455 654 123 88 47 50 41 40 1275 180 2.08 .481 .895 .679 .68 3.268 80 258 .429 .88 100 1130 9260 77 87 88 98 -100 675 182 493 .572 283 101 1.747 1.065 .091 -.805
4 144 191 136 161 8 30 144 177 162 196 8 16 0 0 37 77 147 167 0 3 0 0 38 24 .267 3.75 2 2.073 2.796 4.964 80 309 1.328 .84 100 1230 9240 75 85 98 108 -50 227 192 36 4.464 211 19 .224 2.381 1.252 2.158
5 584 1791 130 164 454 1627 618 1977 172 210 488 1813 0 0 204 708 167 206 88 92 82 90 2081 2301 .279 3.584 3.715 3.276 3.432 1.682 52 160 3.687 .89 80 1400 9270 79 87 116 124 0 2132 195 1937 4.266 2354 2158 .234 4.423 2.093 2.145 2.093
6 138 174 142 170 -4 4 135 169 161 186 -7 -1 0 0 28 64 99 80 0 11 0 0 0 -8 null null null 2.752 2.675 3.171 80 241 1.316 .48 100 1510 9240 75 85 126 136 -50 207 202 5 null 201 null null null null null
7 294 310 138 167 156 143 179 214 188 307 41 47 0 0 217 214 193 763 30 2 17 0 299 88 1.091 .917 1.146 1.181 1.217 3.058 80 328 3.687 .44 100 1640 9240 75 85 139 149 -50 369 199 170 1.091 255 56 .916 1.365 .449 .126
8 715 686 132 165 583 521 721 667 203 276 589 502 0 0 132 150 270 630 96 25 62 0 1104 1091 1.119 .894 .852 .876 .885 1.4 32 136 .756 .88 70 1820 9260 78 85 158 165 -100 817 196 620 1.064 794 598 .94 1.015 .021 .089
9 267 194 135 148 132 46 205 190 163 175 70 42 0 0 165 87 197 131 26 12 10 2 178 112 2.87 .348 .6 .575 .567 3.906 80 366 .359 .57 100 1910 9240 75 85 166 176 -50 231 176 55 .415 226 50 2.41 .714 -.485 -1.269
10 248 279 158 174 90 105 243 245 176 189 85 71 0 0 30 108 63 79 91 41 8 33 195 156 .857 1.167 .835 1.009 1.246 3.872 12 99 3.507 .38 50 2060 9250 78 83 183 188 -100 332 207 125 1.389 292 85 .72 .994 -.008 .474
11 1825 377 136 159 1689 218 1801 369 143 164 1665 210 0 0 392 108 55 72 100 92 100 69 1907 1875 7.748 .129 .126 .114 .127 1.872 52 291 .121 .74 90 2200 9240 75 84 195 204 0 449 189 260 .154 439 250 6.508 .15 -2.702 -2.736 -2.702
12 386 330 149 158 237 172 385 322 154 168 236 164 0 0 76 96 43 61 100 90 100 68 409 400 1.378 .726 .695 .655 .717 2.191 32 138 .971 .59 60 2320 9240 77 83 209 215 0 393 188 205 .864 383 195 1.157 .827 -.211 -.274 -.211
13 314 298 138 155 176 143 308 297 145 174 170 142 0 0 67 111 77 104 94 61 53 28 319 312 1.231 .813 .835 .849 .858 2.012 52 277 1.185 .58 90 2470 9240 75 84 222 231 0 355 185 170 .967 354 169 1.034 .994 -.048 -.008 -.048
14 343 246 138 159 205 87 335 216 149 179 197 57 0 0 75 99 88 116 98 34 59 5 292 254 2.356 .424 .289 .409 .496 2.293 52 198 .712 .46 80 2590 9250 77 85 235 243 0 293 189 104 .505 257 68 1.979 .344 -.985 -1.538 -.985
15 214 192 148 152 66 40 191 188 148 162 43 36 0 0 85 82 35 60 55 33 33 15 106 79 1.65 .606 .837 1.024 .893 3.66 80 281 1.243 .42 100 2730 9240 75 85 248 258 -50 229 181 48 .722 224 43 1.386 .997 -.005 -.471
16 1220 1310 141 154 1079 1156 1203 1333 145 162 1062 1179 0 0 210 320 40 68 100 100 100 100 2235 2241 .933 1.071 1.11 1.044 1.056 1.293 80 237 1.134 .94 100 2870 9250 76 86 262 272 0 1560 183 1376 1.275 1587 1404 .784 1.322 .351 .402 .351
17 419 310 142 157 277 153 412 280 146 163 270 123 0 0 101 115 44 89 100 67 98 40 430 393 1.81 .552 .456 .436 .539 2.895 52 184 .669 .6 80 2990 9250 77 85 275 283 0 369 187 182 .658 333 146 1.521 .542 -.605 -.883 -.605
18 257 181 135 152 122 29 263 177 160 172 128 25 0 0 75 71 138 109 43 10 2 2 151 153 4.207 .238 .195 .327 .293 3.01 80 363 .463 .35 100 3140 9240 75 85 289 299 -50 215 181 35 .283 211 30 3.534 .233 -2.105 -1.821
19 236 281 129 151 107 130 224 264 173 175 95 113 0 0 55 98 199 113 5 46 0 15 237 208 .823 1.215 1.189 1.044 1.19 3.125 52 217 1.194 .64 80 3260 9240 76 84 302 310 -100 335 180 155 1.446 314 135 .691 1.416 .502 .532
20 881 665 131 139 750 526 844 640 156 158 713 501 0 0 178 157 134 92 100 100 100 100 1276 1214 1.426 .701 .703 .689 .725 1.395 52 185 .723 .87 80 3400 9240 76 84 316 324 0 792 165 626 .835 762 596 1.198 .837 -.26 -.258 -.26

Total number of rows: 44160

Table truncated, full table size 9566 Kbytes.




Supplementary data files not provided
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