NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM39920 Query DataSets for GSM39920
Status Public on Feb 21, 2005
Title Salivary gland, parotid 0493
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Salivary gland, parotid 0493
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-09/20446.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
1 325 358 126 135 199 223 309 363 130 146 183 228 0 0 89 117 40 63 100 87 93 81 422 411 .892 1.121 1.246 1.085 1.122 1.674 32 219 1.18 .73 70 1360 7550 47 54 53 60 0 286 108 178 .896 290 182 1.115 .997 -.158 -.005 -.158
2 245 208 127 129 118 79 254 200 129 140 127 71 0 0 62 63 35 64 84 61 76 19 197 198 1.494 .669 .559 .712 .64 2.297 52 296 .959 .47 80 1510 7540 46 54 68 76 0 166 103 63 .536 160 57 1.867 .447 -.901 -1.161 -.901
3 794 720 126 129 668 591 810 727 132 140 684 598 0 0 216 243 37 69 100 100 100 98 1259 1282 1.13 .885 .874 .844 .862 1.545 52 262 .917 .91 80 1660 7540 46 54 83 91 0 576 103 473 .708 582 478 1.413 .699 -.499 -.516 -.499
4 2342 7450 127 131 2215 7319 1944 5900 131 137 1817 5769 0 0 1839 6106 37 52 95 100 93 98 9534 7586 .303 3.304 3.175 3.404 3.297 1.837 80 426 3.388 .97 100 1800 7540 45 55 96 106 0 5960 105 5855 2.643 4720 4615 .378 2.54 1.402 1.345 1.402
5 396 442 128 136 268 306 402 439 133 142 274 303 0 0 119 169 36 58 100 90 96 84 574 577 .876 1.142 1.106 .999 1.16 2.019 32 212 1.299 .76 70 1950 7540 46 53 112 119 0 354 109 245 .913 351 242 1.095 .885 -.131 -.177 -.131
6 265 207 126 133 139 74 272 200 129 141 146 67 0 0 77 82 34 55 86 57 80 34 213 213 1.878 .532 .459 .552 .573 2.291 52 285 .844 .4 80 2100 7540 46 54 127 135 0 166 106 59 .426 160 54 2.348 .367 -1.231 -1.446 -1.231
7 505 240 135 137 370 103 491 240 137 147 356 103 0 0 154 78 34 54 100 75 100 42 473 459 3.592 .278 .289 .269 .272 1.991 52 222 .258 .6 80 2240 7540 46 54 141 149 0 192 110 82 .223 192 82 4.49 .231 -2.167 -2.111 -2.167
8 2921 8308 133 125 2788 8183 2969 8482 137 138 2836 8357 0 0 1953 5801 39 69 96 96 95 92 10971 11193 .341 2.935 2.947 2.505 2.761 1.872 80 438 3.033 .96 110 2380 7530 43 54 153 164 0 6646 100 6546 2.348 6786 6686 .426 2.357 1.231 1.237 1.231
9 467 647 129 116 338 531 499 669 134 126 370 553 0 0 145 207 37 68 98 94 96 92 869 923 .637 1.571 1.495 1.612 1.455 1.662 52 274 1.623 .89 80 2530 7540 46 54 170 178 0 518 93 425 1.257 535 442 .796 1.196 .33 .258 .33
10 296 288 122 125 174 163 306 277 128 135 184 152 0 0 81 92 36 58 96 90 84 78 337 336 1.067 .937 .826 .96 .965 1.839 32 206 1.094 .66 70 2680 7540 46 53 185 192 0 230 100 130 .749 222 122 1.334 .661 -.416 -.598 -.416
11 726 801 128 136 598 665 686 642 129 142 558 506 0 0 363 483 33 51 98 92 96 90 1263 1064 .899 1.112 .907 1.002 1.07 1.725 52 279 1.209 .9 80 2820 7540 46 54 199 207 0 641 109 532 .89 514 405 1.124 .725 -.169 -.463 -.169
12 897 819 128 143 769 676 943 877 131 149 815 734 0 0 264 257 33 53 100 96 100 94 1445 1549 1.138 .879 .901 .864 .876 1.399 52 264 .884 .95 80 2970 7540 46 54 214 222 0 655 114 541 .703 702 587 1.422 .72 -.508 -.473 -.508
13 492 488 128 143 364 345 484 499 132 149 356 356 0 0 156 169 36 57 98 92 96 90 709 712 1.055 .948 1 .878 .943 1.806 52 254 .977 .85 80 3110 7540 46 54 228 236 0 390 114 276 .758 399 285 1.319 .8 -.399 -.322 -.399
14 311 624 131 144 180 480 296 633 134 156 165 489 0 0 87 218 33 58 100 94 88 94 660 654 .375 2.667 2.964 2.697 2.875 1.801 52 267 2.824 .83 80 3250 7540 46 54 242 250 0 499 115 384 2.133 506 391 .469 2.371 1.093 1.245 1.093
15 3061 4755 120 140 2941 4615 3453 5158 128 146 3333 5018 0 0 1729 2785 37 50 97 100 96 100 7556 8351 .637 1.569 1.506 1.55 1.542 1.678 80 431 1.599 .98 100 3410 7540 45 55 257 267 0 3804 112 3692 1.255 4126 4014 .797 1.204 .328 .268 .328
16 1003 1945 121 137 882 1808 1041 2068 125 142 920 1931 0 0 284 545 32 47 100 100 96 100 2690 2851 .488 2.05 2.099 2.064 2.081 1.31 52 324 2.089 .96 90 3550 7540 45 54 271 280 0 1556 110 1446 1.64 1654 1545 .61 1.679 .714 .748 .714
17 228 274 121 149 107 125 235 282 126 152 114 133 0 0 47 80 29 54 96 81 87 56 232 247 .856 1.168 1.167 1.147 1.094 1.878 32 232 1.775 .62 70 3710 7540 46 53 288 295 0 219 119 100 .935 226 106 1.07 .933 -.098 -.1 -.098
18 245 226 125 132 120 94 247 230 125 140 122 98 0 0 78 56 29 47 90 81 84 53 214 220 1.277 .783 .803 .723 .828 2.073 32 228 .929 .58 70 3850 7540 46 53 302 309 0 181 106 75 .627 184 78 1.596 .643 -.674 -.638 -.674
19 594 811 121 143 473 668 639 874 125 146 518 731 0 0 212 318 36 49 93 93 93 93 1141 1249 .708 1.412 1.411 1.345 1.311 1.489 32 191 1.465 .91 70 3990 7550 47 54 316 323 0 649 114 534 1.13 699 585 .885 1.129 .176 .175 .176
20 249 279 125 142 124 137 269 272 127 150 144 130 0 0 82 89 29 52 86 86 80 67 261 274 .905 1.105 .903 1.047 .953 2.059 52 255 1.284 .6 80 4130 7540 46 54 330 338 0 223 114 110 .884 218 104 1.131 .722 -.178 -.469 -.178

Total number of rows: 43008

Table truncated, full table size 9239 Kbytes.




Supplementary data files not provided

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap