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Sample GSM39900 Query DataSets for GSM39900
Status Public on Feb 21, 2005
Title Salivary gland, parotid 0506
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Salivary gland, parotid 0506
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-09/20436.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 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
1 384 446 128 89 256 357 400 479 131 95 272 390 0 0 158 203 34 34 92 94 88 90 613 662 .717 1.395 1.434 1.421 1.413 2.304 52 356 1.433 .8 90 1380 7910 34 43 57 66 0 330 66 264 1.033 355 289 .968 1.062 .047 .087 .047
2 320 200 143 100 177 100 328 194 146 106 185 94 0 0 90 61 37 47 94 80 84 50 277 279 1.77 .565 .508 .541 .527 1.968 52 282 .526 .61 80 1530 7910 35 43 73 81 0 148 74 74 .418 144 70 2.39 .376 -1.257 -1.41 -1.257
3 1449 1322 145 99 1304 1223 1532 1206 145 102 1387 1107 0 0 547 706 36 32 100 100 100 98 2527 2494 1.066 .938 .798 .819 .955 1.931 52 311 1.04 .91 90 1690 7910 34 43 88 97 0 979 73 906 .695 893 820 1.439 .591 -.525 -.758 -.525
4 4355 8422 142 103 4213 8319 4286 9495 144 106 4144 9392 0 0 2187 4258 35 36 100 100 100 100 12532 13536 .506 1.975 2.266 1.934 1.955 1.507 52 321 2.039 .94 90 1820 7910 34 43 101 110 0 6239 76 6162 1.463 7033 6957 .684 1.679 .549 .747 .549
5 448 476 137 103 311 373 488 494 142 106 351 391 0 0 195 166 33 38 86 98 82 94 684 742 .834 1.199 1.114 1.359 1.161 2.239 52 266 1.112 .87 80 1970 7920 36 44 117 125 0 353 76 276 .888 366 290 1.126 .825 -.171 -.277 -.171
6 299 258 135 102 164 156 309 259 137 108 174 157 0 0 88 106 29 36 90 84 87 81 320 331 1.051 .951 .902 .82 .904 2.019 32 212 1.167 .69 70 2110 7920 36 43 131 138 0 191 76 116 .705 192 116 1.419 .668 -.505 -.581 -.505
7 534 392 131 106 403 286 590 398 137 113 459 292 0 0 244 164 35 41 90 91 85 86 689 751 1.409 .71 .636 .724 .724 2.207 80 334 .647 .81 100 2260 7920 35 45 145 155 0 290 79 212 .526 295 216 1.902 .471 -.928 -1.085 -.928
8 4056 15905 134 107 3922 15798 4184 17643 138 118 4050 17536 0 0 1454 6861 36 46 100 100 100 100 19720 21586 .248 4.028 4.33 3.979 4.2 1.531 52 271 4.521 .93 90 2410 7910 34 43 160 169 0 11781 79 11702 2.984 13069 12990 .335 3.207 1.577 1.681 1.577
9 903 1656 139 103 764 1553 1038 1799 140 109 899 1696 0 0 380 597 32 36 94 100 94 100 2317 2595 .492 2.033 1.887 2.208 1.943 2.114 52 254 2.046 .9 80 2550 7920 36 44 175 183 0 1227 76 1150 1.506 1333 1256 .664 1.397 .59 .483 .59
10 293 320 148 100 145 220 299 320 151 107 151 220 0 0 107 88 35 37 75 98 71 96 365 371 .659 1.517 1.457 1.823 1.366 2.962 52 254 1.318 .71 80 2700 7920 36 44 190 198 0 237 74 163 1.124 237 163 .89 1.079 .168 .11 .168
11 1047 1136 147 97 900 1039 1063 1148 147 101 916 1051 0 0 567 576 34 36 98 100 94 100 1939 1967 .866 1.154 1.147 1.217 1.145 2.3 52 254 1.113 .91 80 2840 7920 36 44 204 212 0 841 72 770 .855 850 779 1.169 .85 -.226 -.235 -.226
12 1217 1353 137 106 1080 1247 1185 1489 139 107 1048 1383 0 0 350 525 36 33 100 100 100 100 2327 2431 .866 1.155 1.32 1.078 1.201 1.769 52 313 1.271 .91 90 2990 7910 34 43 218 227 0 1002 79 924 .855 1103 1024 1.169 .978 -.226 -.033 -.226
13 780 992 147 101 633 891 816 1011 151 106 669 910 0 0 316 373 38 33 94 100 94 100 1524 1579 .71 1.408 1.36 1.625 1.32 2.381 52 254 1.394 .89 80 3130 7920 36 44 233 241 0 735 75 660 1.043 749 674 .959 1.008 .06 .011 .06
14 327 722 143 108 184 614 316 759 149 114 173 651 0 0 115 316 35 40 92 100 84 96 798 824 .3 3.337 3.763 3.182 3.33 2.114 52 254 3.707 .79 80 3280 7920 36 44 248 256 0 535 80 455 2.472 562 482 .405 2.787 1.306 1.479 1.306
15 4880 17037 133 115 4747 16922 5298 16908 138 127 5165 16793 0 0 1768 7368 39 54 100 100 100 100 21669 21958 .281 3.565 3.251 3.452 3.461 1.551 52 333 4.037 .92 90 3420 7910 34 43 261 270 0 12620 85 12535 2.641 12524 12439 .379 2.408 1.401 1.268 1.401
16 1692 5299 131 108 1561 5191 1754 5872 135 115 1623 5764 0 0 457 1868 39 42 100 100 100 100 6752 7387 .301 3.325 3.551 3.184 3.277 1.463 52 345 3.839 .92 90 3570 7910 34 43 276 285 0 3925 80 3845 2.463 4350 4270 .406 2.631 1.301 1.395 1.301
17 262 213 137 109 125 104 262 214 140 113 125 105 0 0 81 57 35 38 90 90 78 68 229 230 1.202 .832 .84 .975 1.048 2.382 32 214 .705 .53 70 3730 7920 36 43 293 300 0 158 81 77 .616 159 78 1.623 .622 -.698 -.684 -.698
18 268 157 134 101 134 56 264 153 139 107 130 52 0 0 88 57 36 48 87 56 75 25 190 182 2.393 .418 .4 .555 .522 2.975 32 208 .417 .41 70 3860 7920 36 43 306 313 0 116 75 41 .31 113 39 3.23 .296 -1.692 -1.755 -1.692
19 721 1029 132 99 589 930 605 860 136 105 473 761 0 0 391 656 36 47 98 96 96 96 1519 1234 .633 1.579 1.609 1.527 1.544 2.093 52 287 1.707 .93 80 4010 7920 36 44 321 329 0 762 73 689 1.17 637 564 .855 1.192 .226 .253 .226
20 283 247 128 100 155 147 283 242 131 106 155 142 0 0 93 79 36 44 86 92 84 78 302 297 1.054 .948 .916 .851 .728 2.351 52 328 .914 .59 90 4160 7920 35 44 335 344 0 183 74 109 .703 179 105 1.423 .679 -.509 -.559 -.509

Total number of rows: 43008

Table truncated, full table size 9487 Kbytes.




Supplementary data files not provided

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