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Sample GSM39914 Query DataSets for GSM39914
Status Public on Feb 21, 2005
Title Small bowel, duodenum 0825
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Small bowel, duodenum 0825
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-03/26256.gif
 
Submission date Jan 26, 2005
Last update date Nov 22, 2005
Contact name Jonathan Pollack
E-mail(s) [email protected]
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 GPL1823
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
1 515 287 216 184 299 103 502 297 218 188 286 113 0 0 105 52 53 79 100 78 100 9 402 399 2.903 .344 .395 .358 .405 1.631 32 191 .341 .69 70 1760 7310 47 54 48 55 0 259 166 93 .31 268 102 3.222 .356 -1.688 -1.49 -1.688
2 314 209 202 246 112 -37 290 200 206 252 88 -46 0 0 113 81 49 70 68 8 45 3 75 42 null null null .717 .762 7.251 80 415 1.893 .23 100 1880 7300 45 55 59 69 -50 188 222 -33 null 180 null null null null null
3 1198 2463 187 332 1011 2131 1219 2400 194 333 1032 2068 0 0 252 378 53 61 100 100 100 100 3142 3100 .474 2.108 2.004 2.158 2.217 1.34 52 229 2.149 .93 80 2060 7320 48 56 78 86 0 2219 299 1920 1.899 2162 1863 .527 1.805 .925 .852 .925
4 3382 5846 196 390 3186 5456 3611 6355 204 395 3415 5965 0 0 1934 2799 51 75 98 100 96 100 8642 9380 .584 1.712 1.747 2.034 1.749 2.068 80 327 1.662 .96 100 2200 7310 46 56 91 101 0 5267 351 4915 1.543 5725 5374 .648 1.574 .626 .654 .626
5 595 834 201 449 394 385 588 828 207 454 387 379 0 0 136 139 48 82 96 100 96 98 779 766 1.023 .977 .979 1.009 .938 1.998 52 223 1.179 .67 90 2350 7310 46 55 106 115 0 751 405 347 .88 746 341 1.136 .882 -.184 -.181 -.184
6 323 425 210 481 113 -56 306 428 214 490 96 -53 0 0 111 116 53 84 61 10 46 2 57 43 null null null .952 .745 4.632 80 356 .851 .2 100 2460 7300 45 55 117 127 -50 383 433 -50 null 386 null null null null null
7 886 444 202 501 684 -57 874 413 207 503 672 -88 0 0 279 138 55 92 100 15 100 9 627 584 null null null .19 .156 5.965 52 240 7.555 .36 80 2640 7310 47 55 136 144 0 400 451 -51 null 372 null null null null null null
8 4021 6378 211 476 3810 5902 4009 6301 230 482 3798 5825 0 0 1544 1643 128 153 98 100 98 100 9712 9623 .646 1.549 1.534 1.72 1.545 1.636 52 275 1.474 .95 90 2780 7320 47 56 149 158 0 5746 429 5317 1.396 5677 5248 .717 1.382 .481 .466 .481
9 1125 1726 226 570 899 1156 1118 1718 244 568 892 1148 0 0 167 229 99 167 100 100 100 100 2055 2040 .778 1.286 1.287 1.278 1.332 1.309 32 184 1.431 .87 70 2920 7320 48 55 164 171 0 1555 514 1041 1.158 1548 1034 .863 1.159 .212 .213 .212
10 329 724 208 650 121 74 318 691 220 610 110 41 0 0 115 149 69 200 65 18 38 5 195 151 1.635 .612 .373 .881 1.023 3.99 80 375 4.526 .15 100 3050 7300 45 55 176 186 -50 652 586 67 .551 623 37 1.815 .336 -1.574 -.86
11 1116 1291 218 687 898 604 1079 1300 223 697 861 613 0 0 259 162 60 103 100 100 100 100 1502 1474 1.487 .673 .712 .677 .677 1.443 32 187 .659 .85 70 3220 7320 48 55 194 201 0 1163 619 544 .606 1171 552 1.65 .641 -.723 -.641 -.723
12 1158 1306 215 713 943 593 1179 1330 222 724 964 617 0 0 236 195 61 104 100 98 100 96 1536 1581 1.59 .629 .64 .593 .617 1.72 52 203 .66 .85 80 3360 7310 47 55 208 216 0 1177 642 534 .567 1198 556 1.765 .577 -.82 -.794 -.82
13 475 698 224 719 251 -21 409 693 226 736 185 -26 0 0 285 111 59 135 57 5 55 1 230 159 null null null .478 .277 5.682 80 302 .165 .25 100 3480 7300 45 55 219 229 -50 629 648 -19 null 624 null null null null null
14 314 534 224 744 90 -210 276 539 230 745 52 -205 0 0 116 170 66 156 47 1 36 0 -120 -153 null null null 2.344 2.614 3.935 80 342 .307 .41 100 3630 7300 45 55 234 244 -50 481 670 -189 null 486 null null null null null
15 4571 8982 220 658 4351 8324 5006 8981 226 668 4786 8323 0 0 1650 2065 64 148 100 100 100 100 12675 13109 .523 1.913 1.739 2.119 1.909 1.621 52 256 1.86 .94 90 3800 7320 47 56 251 260 0 8092 593 7499 1.724 8091 7498 .58 1.567 .785 .648 .785
16 1322 2148 219 532 1103 1616 1321 2155 223 534 1102 1623 0 0 250 248 61 109 100 100 100 100 2719 2725 .683 1.465 1.473 1.504 1.453 1.376 52 185 1.489 .91 80 3940 7320 48 56 266 274 0 1935 479 1456 1.32 1941 1462 .758 1.327 .4 .408 .4
17 253 325 215 436 38 -111 247 314 220 453 32 -122 0 0 69 94 58 95 35 2 11 0 -73 -90 null null null 2.86 2.8 3.595 80 280 .227 .26 100 4070 7300 45 55 278 288 -50 293 393 -100 null 283 null null null null null
18 281 295 207 388 74 -93 261 292 219 389 54 -96 0 0 92 92 70 76 42 5 23 0 -19 -42 null null null 1.354 1.449 2.568 80 349 .703 .36 100 4210 7300 45 55 292 302 -50 266 350 -84 null 263 null null null null null
19 698 704 201 354 497 350 769 685 229 359 568 331 0 0 230 149 100 73 90 96 90 93 847 899 1.42 .704 .583 .761 .705 2.019 32 186 .649 .79 70 4380 7330 49 56 310 317 0 634 319 315 .634 617 298 1.576 .525 -.656 -.93 -.656
20 255 299 203 340 52 -41 250 297 214 343 47 -43 0 0 74 76 73 77 36 5 13 1 11 4 null null null 1.291 1.829 5.12 80 363 .772 .16 100 4500 7290 44 54 321 331 -50 269 306 -37 null 268 null null null null null

Total number of rows: 43008

Table truncated, full table size 9439 Kbytes.




Supplementary data files not provided
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