NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM39891 Query DataSets for GSM39891
Status Public on Feb 21, 2005
Title Salivary gland, parotid 1762
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Salivary gland parotid 1762
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-01/24158.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
1 567 413 252 177 315 236 614 409 259 184 362 232 0 0 170 107 57 50 87 100 87 90 551 594 1.335 .749 .641 .619 .668 1.675 32 219 .676 .7 70 1360 7460 46 53 48 55 0 275 118 157 .499 273 155 2.002 .427 -1.002 -1.227 -1.002
2 436 263 252 188 184 75 469 259 257 190 217 71 0 0 132 74 53 52 80 59 76 32 259 288 2.453 .408 .327 .368 .356 4.13 52 349 .198 .25 90 1510 7450 44 53 62 71 0 175 125 50 .272 173 47 3.68 .218 -1.88 -2.197 -1.88
3 1330 1511 257 195 1073 1316 1428 1687 261 200 1171 1492 0 0 408 573 51 55 100 98 96 98 2389 2663 .815 1.226 1.274 1.18 1.206 2.644 52 314 1.339 .88 90 1660 7450 44 53 77 86 0 1007 130 877 .818 1125 995 1.223 .849 -.29 -.235 -.29
4 3069 12157 263 201 2806 11956 3488 12612 263 207 3225 12411 0 0 1566 5369 58 50 96 100 96 100 14762 15636 .235 4.261 3.848 4.7 4.247 2.053 52 281 4.434 .89 80 1790 7460 46 54 91 99 0 8105 134 7971 2.841 8408 8274 .352 2.566 1.506 1.359 1.506
5 612 616 276 206 336 410 647 636 281 209 371 430 0 0 209 150 52 59 87 100 87 93 746 801 .82 1.22 1.159 1.094 1.071 1.556 32 170 1.153 .75 60 1940 7460 47 53 107 113 0 411 137 273 .813 424 287 1.229 .773 -.298 -.372 -.298
6 494 281 274 206 220 75 504 276 275 206 230 70 0 0 162 78 53 56 88 55 82 23 295 300 2.933 .341 .304 .32 .312 2.583 52 295 .343 .4 80 2090 7450 45 53 121 129 0 187 137 50 .227 184 47 4.4 .203 -2.138 -2.301 -2.138
7 685 382 264 200 421 182 720 385 270 204 456 185 0 0 208 81 52 56 92 92 92 78 603 641 2.313 .432 .406 .418 .408 1.965 52 259 .351 .67 90 2240 7460 45 54 135 144 0 255 133 121 .288 257 123 3.47 .27 -1.795 -1.886 -1.795
8 2976 10683 276 206 2700 10477 2943 10155 274 212 2667 9949 0 0 1225 3421 54 56 100 100 100 100 13177 12616 .258 3.88 3.73 4.262 3.769 1.573 52 268 3.826 .92 90 2380 7460 45 54 149 158 0 7122 137 6985 2.587 6770 6633 .387 2.487 1.371 1.314 1.371
9 946 1065 276 200 670 865 1011 1136 275 209 735 936 0 0 325 417 55 60 90 100 90 98 1535 1671 .775 1.291 1.273 1.437 1.213 2.674 52 285 1.326 .89 80 2530 7460 46 54 165 173 0 710 133 577 .861 757 624 1.162 .849 -.216 -.236 -.216
10 508 385 279 194 229 191 533 392 280 205 254 198 0 0 130 103 57 56 90 87 84 84 420 452 1.199 .834 .78 .808 .854 2.446 32 219 .777 .55 70 2680 7450 45 52 180 187 0 257 129 127 .556 261 132 1.798 .52 -.847 -.944 -.847
11 971 920 281 219 690 701 1033 982 284 227 752 763 0 0 334 331 59 62 88 100 88 100 1391 1515 .984 1.016 1.015 .999 .962 2.09 52 279 1.03 .87 80 2820 7460 46 54 194 202 0 613 146 467 .677 655 509 1.476 .676 -.562 -.564 -.562
12 1052 792 287 223 765 569 1091 834 294 228 804 611 0 0 306 302 61 58 96 98 94 94 1334 1415 1.344 .744 .76 .676 .712 2.579 52 274 .783 .86 80 2970 7450 45 53 209 217 0 528 149 379 .496 556 407 2.017 .507 -1.012 -.981 -1.012
13 773 676 282 230 491 446 764 686 288 236 482 456 0 0 248 234 54 68 94 94 92 86 937 938 1.101 .908 .946 .854 .92 2.174 52 256 .929 .82 80 3110 7450 45 53 223 231 0 451 153 297 .606 457 304 1.651 .631 -.724 -.665 -.724
14 488 881 290 232 198 649 497 870 291 242 207 638 0 0 155 328 57 66 82 96 73 96 847 845 .305 3.278 3.082 3.562 3.243 2.514 52 252 3.464 .69 80 3260 7460 46 54 238 246 0 587 155 433 2.185 580 425 .458 2.055 1.128 1.039 1.128
15 3123 6768 289 250 2834 6518 3192 7142 292 261 2903 6892 0 0 1051 2340 57 74 100 100 98 100 9352 9795 .435 2.3 2.374 2.392 2.362 1.726 52 316 2.338 .95 90 3410 7460 45 54 252 261 0 4512 167 4345 1.533 4761 4595 .652 1.583 .617 .662 .617
16 1441 3084 296 261 1145 2823 1650 3485 296 271 1354 3224 0 0 571 1297 61 79 94 98 94 98 3968 4578 .406 2.466 2.381 2.318 2.34 1.65 52 326 2.493 .9 90 3550 7460 45 54 266 275 0 2056 174 1882 1.644 2323 2149 .608 1.587 .717 .667 .717
17 505 286 296 257 209 29 526 285 301 259 230 28 0 0 123 79 54 68 90 31 81 12 238 258 7.207 .139 .122 .286 .326 2.932 32 216 .133 .12 70 3710 7460 46 53 283 290 0 191 171 19 .093 190 19 10.81 .081 -3.434 -3.623 -3.434
18 493 246 294 246 199 0 490 248 293 253 196 2 0 0 165 64 56 64 84 15 78 0 199 198 null null .01 .183 .214 2.143 32 172 10.95 .15 60 3840 7450 46 52 297 303 0 164 164 0 null 165 1 null .007 null -7.2 null
19 715 769 270 221 445 548 715 801 271 229 445 580 0 0 235 368 52 63 94 90 94 88 993 1025 .812 1.231 1.303 1.027 1.136 1.825 52 291 1.399 .84 80 3990 7450 45 53 311 319 0 513 147 365 .821 534 387 1.218 .869 -.285 -.203 -.285
20 451 289 267 215 184 74 480 297 267 224 213 82 0 0 129 79 53 64 84 56 81 21 258 295 2.486 .402 .385 .355 .345 2.561 32 198 .141 .12 70 4130 7450 45 52 325 332 0 193 143 49 .268 198 55 3.73 .257 -1.899 -1.962 -1.899

Total number of rows: 43008

Table truncated, full table size 9408 Kbytes.




Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap