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Sample GSM39990 Query DataSets for GSM39990
Status Public on Feb 21, 2005
Title Pancreas 0432
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Pancreas 0432
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://jdemeter-smd.stanford.edu:8000/MicroArray/gifs/2001-04/15160.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
1 195 164 145 138 50 26 173 166 155 144 28 28 0 0 73 70 47 55 36 35 26 10 76 56 1.923 .52 1 .853 .781 3.158 80 413 .815 .35 100 760 8030 90 100 51 61 -100 202 170 32 .642 205 35 1.558 1.235 .304 -.639
2 280 528 151 170 129 358 218 356 165 188 67 186 0 0 160 369 69 169 50 53 31 46 487 253 .36 2.775 2.776 2.73 2.762 2.153 32 113 2.851 .87 60 920 8070 96 102 69 75 -100 652 210 442 3.426 440 230 .292 3.427 1.777 1.777
3 1553 915 151 146 1402 769 1588 893 156 165 1437 747 0 0 466 311 53 126 98 100 98 93 2171 2184 1.823 .549 .52 .547 .524 1.497 80 243 .529 .91 100 1050 8080 95 105 80 90 0 1130 180 949 .677 1102 922 1.477 .642 -.562 -.64 -.562
4 196 287 143 143 53 144 161 185 154 165 18 42 0 0 115 255 60 104 28 31 15 25 197 60 .368 2.717 2.333 2.515 2.8 3.18 32 139 1.588 .82 70 1180 8070 95 102 94 101 -100 354 177 178 3.354 228 52 .298 2.881 1.526 1.746
5 531 640 143 145 388 495 521 628 151 161 378 483 0 0 135 183 52 90 98 96 97 95 883 861 .784 1.276 1.278 1.254 1.27 1.511 80 222 1.369 .89 100 1330 8070 94 104 108 118 0 790 179 611 1.575 775 596 .635 1.578 .655 .658 .655
6 144 157 142 134 2 23 142 147 149 145 0 13 0 0 30 64 53 77 5 18 0 2 25 13 .087 11.5 null 1.3 1.681 5.122 80 290 1.903 .42 100 1440 8030 90 100 119 129 -50 194 165 28 14.198 181 16 .07 null null 3.828
7 460 316 143 139 317 177 495 320 153 153 352 181 0 0 136 120 57 80 92 76 87 58 494 533 1.791 .558 .514 .544 .57 1.838 80 238 .656 .67 100 1610 8070 94 104 136 146 0 390 172 219 .689 395 223 1.451 .635 -.537 -.656 -.537
8 557 893 143 139 414 754 553 886 155 155 410 747 0 0 149 304 62 91 97 98 97 97 1168 1157 .549 1.821 1.822 1.797 1.788 1.517 80 226 2.117 .84 100 1740 8070 94 104 149 159 0 1102 172 931 2.248 1094 922 .445 2.249 1.169 1.169 1.169
9 380 180 135 136 245 44 370 156 150 155 235 20 0 0 141 81 63 89 90 21 75 6 289 255 5.568 .18 .085 .21 .29 3.554 32 202 .182 .21 70 1880 8030 91 98 164 171 0 222 168 54 .222 193 25 4.51 .105 -2.173 -3.251 -2.173
10 248 192 142 147 106 45 243 181 144 154 101 34 0 0 53 71 33 62 96 31 75 12 151 135 2.356 .425 .337 .6 .673 2.495 32 166 3.736 .1 70 2020 8040 92 99 178 185 0 237 181 56 .524 223 42 1.908 .416 -.932 -1.267 -.932
11 1040 10908 142 139 898 10769 1073 11338 144 146 931 11199 0 0 289 3710 33 54 100 100 100 100 11667 12130 .083 11.992 12.029 11.731 12.117 1.362 80 281 12.525 .97 100 2140 8030 90 100 189 199 0 13467 172 13295 14.805 13998 13826 .068 14.851 3.888 3.892 3.888
12 315 320 145 140 170 180 305 305 149 146 160 165 0 0 88 113 34 52 98 86 96 73 350 325 .944 1.059 1.031 .963 1.189 2.138 52 180 1.278 .63 80 2260 8030 91 99 202 210 0 395 173 222 1.307 377 204 .765 1.273 .386 .348 .386
13 338 310 145 144 193 166 343 294 154 151 198 150 0 0 65 116 71 62 98 80 76 65 359 348 1.163 .86 .758 .813 .918 2.379 52 200 1.01 .62 80 2400 8030 91 99 216 224 0 383 178 205 1.062 363 185 .942 .935 .087 -.097 .087
14 504 316 146 133 358 183 500 315 152 143 354 182 0 0 119 100 64 65 100 87 98 65 541 536 1.956 .511 .514 .457 .501 1.945 80 277 .516 .71 100 2540 8040 91 101 229 239 0 390 164 226 .631 389 225 1.585 .635 -.664 -.656 -.664
15 361 253 150 139 211 114 353 234 151 143 203 95 0 0 68 84 37 61 100 71 100 40 325 298 1.851 .54 .468 .397 .536 3.323 32 171 .698 .57 70 2670 8020 90 97 243 250 0 312 172 141 .667 289 117 1.499 .578 -.584 -.791 -.584
16 1152 796 145 130 1007 666 1147 788 148 135 1002 658 0 0 173 260 33 56 100 100 100 98 1673 1660 1.512 .661 .657 .61 .638 1.487 80 332 .7 .9 110 2810 8040 90 101 255 266 0 983 160 822 .817 973 812 1.225 .811 -.292 -.303 -.292
17 464 415 138 132 326 283 463 402 141 138 325 270 0 0 80 120 31 56 100 98 100 94 609 595 1.152 .868 .831 .839 .876 1.519 52 209 .931 .78 90 2930 8030 90 99 268 277 0 512 163 349 1.072 496 333 .933 1.026 .1 .037 .1
18 413 183 143 139 270 44 410 171 147 145 267 32 0 0 70 65 32 58 100 37 100 12 314 299 6.136 .163 .12 .191 .216 2.63 80 265 .112 .18 100 3070 8030 90 100 282 292 0 226 172 54 .201 211 40 4.97 .148 -2.313 -2.757 -2.313
19 295 223 149 141 146 82 293 208 153 147 144 67 0 0 51 83 55 60 97 52 76 27 228 211 1.78 .562 .465 .539 .634 2.612 80 250 1.015 .46 100 3200 8030 90 100 295 305 0 275 174 101 .693 257 83 1.442 .574 -.528 -.8 -.528
20 811 832 146 141 665 691 835 836 151 147 689 695 0 0 233 234 53 61 100 98 97 97 1356 1384 .962 1.039 1.009 1.058 1.062 1.736 80 287 1.03 .88 100 3340 8030 90 100 309 319 0 1027 174 853 1.283 1032 858 .78 1.245 .359 .317 .359

Total number of rows: 44160

Table truncated, full table size 9659 Kbytes.




Supplementary data files not provided
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