NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM39893 Query DataSets for GSM39893
Status Public on Feb 21, 2005
Title Uterine corpus, myometriun 1205
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Uterine corpus, myometrium 1205
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-11/21775.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
1 428 1092 170 143 258 949 384 1208 179 148 214 1065 0 0 249 669 66 48 68 88 62 82 1207 1279 .272 3.678 4.977 3.359 3.207 3.274 80 438 3.89 .76 100 1190 7890 40 50 38 48 0 1103 144 959 3.715 1220 1076 .269 5.027 1.894 2.33 1.894
2 382 259 171 152 211 107 373 257 184 160 202 105 0 0 124 59 79 51 93 78 59 53 318 307 1.972 .507 .52 .538 .547 2.45 32 186 .292 .46 70 1330 7910 43 50 53 60 0 262 154 108 .512 260 106 1.952 .525 -.965 -.929 -.965
3 1159 2367 170 157 989 2210 896 2154 178 162 726 1997 0 0 928 1747 67 54 81 91 75 87 3199 2723 .448 2.235 2.751 2.606 2.102 2.451 80 419 2.197 .88 100 1480 7890 40 50 67 77 0 2391 159 2232 2.257 2176 2017 .443 2.778 1.175 1.474 1.175
4 3883 5012 174 151 3709 4861 3714 4082 175 158 3540 3931 0 0 3174 3371 59 55 96 100 94 100 8570 7471 .763 1.311 1.11 1.782 1.438 2.141 52 293 1.196 .96 90 1620 7900 41 50 81 90 0 5063 153 4910 1.324 4123 3971 .755 1.122 .405 .166 .405
5 522 1992 166 159 356 1833 460 2091 174 162 294 1932 0 0 269 1009 55 57 90 93 81 90 2189 2226 .194 5.149 6.571 5.156 5.396 2.039 32 213 4.899 .87 70 1760 7900 42 49 96 103 0 2012 161 1852 5.201 2112 1952 .192 6.638 2.379 2.731 2.379
6 357 294 166 171 191 123 339 293 176 176 173 122 0 0 166 119 61 66 73 65 63 46 314 295 1.553 .644 .705 .773 .751 2.446 52 294 .589 .59 80 1920 7890 41 49 112 120 0 297 173 124 .65 296 123 1.537 .712 -.62 -.489 -.62
7 702 13276 169 178 533 13098 739 14791 177 187 570 14613 0 0 307 6317 66 73 96 100 92 100 13631 15183 .041 24.574 25.637 24.658 25.365 1.546 52 270 28.14 .86 90 2070 7890 40 49 126 135 0 13410 180 13230 24.822 14940 14761 .04 25.896 4.634 4.695 4.634
8 4735 7566 177 175 4558 7391 4953 7587 183 183 4776 7412 0 0 3537 5108 65 63 92 100 92 96 11949 12188 .617 1.622 1.552 1.826 1.646 1.968 80 309 1.578 .95 100 2210 7890 40 50 140 150 0 7642 177 7466 1.638 7664 7487 .611 1.568 .712 .649 .712
9 1006 1516 171 171 835 1345 1103 1561 177 179 932 1390 0 0 495 662 60 56 94 100 94 98 2180 2322 .621 1.611 1.491 1.662 1.548 1.689 52 254 1.568 .93 80 2350 7890 41 49 155 163 0 1531 173 1359 1.627 1577 1404 .615 1.506 .702 .591 .702
10 415 409 159 171 256 238 444 408 166 175 285 237 0 0 180 172 58 49 84 78 81 78 494 522 1.076 .93 .832 .859 .942 2.082 32 213 .894 .75 70 2500 7890 41 48 170 177 0 413 173 240 .939 412 239 1.065 .84 -.091 -.252 -.091
11 1246 1349 172 181 1074 1168 1061 1205 177 186 889 1024 0 0 722 725 64 57 94 96 92 96 2242 1913 .92 1.088 1.152 1.15 1.134 1.8 52 288 1.047 .93 80 2640 7890 41 49 184 192 0 1363 183 1180 1.099 1217 1034 .91 1.163 .136 .218 .136
12 1343 1416 177 194 1166 1222 1475 1534 178 197 1298 1340 0 0 554 593 62 57 92 94 92 94 2388 2638 .954 1.048 1.032 1.035 1.113 1.507 52 264 1.046 .94 80 2800 7890 41 49 200 208 0 1430 196 1234 1.059 1549 1354 .945 1.043 .082 .06 .082
13 765 845 163 195 602 650 773 910 176 199 610 715 0 0 398 448 65 61 90 86 88 84 1252 1325 .926 1.08 1.172 .94 1.002 1.905 52 266 1.127 .9 80 2940 7890 41 49 214 222 0 854 197 657 1.091 919 722 .917 1.184 .125 .244 .125
14 401 458 169 199 232 259 448 531 180 205 279 332 0 0 161 192 65 61 84 84 78 78 491 611 .896 1.116 1.19 1.02 1.214 2.056 32 212 1.096 .7 70 3090 7890 41 48 229 236 0 463 201 262 1.128 536 335 .887 1.202 .173 .265 .173
15 5374 6850 177 195 5197 6655 5829 7660 183 207 5652 7465 0 0 2383 2989 71 77 100 100 98 100 11852 13117 .781 1.281 1.321 1.287 1.27 1.461 52 334 1.284 .97 90 3240 7890 40 49 243 252 0 6919 197 6722 1.293 7737 7540 .773 1.334 .371 .416 .371
16 2499 2893 192 192 2307 2701 2727 3298 193 197 2535 3106 0 0 1103 1194 67 61 94 98 92 96 5008 5641 .854 1.171 1.225 1.133 1.189 1.56 52 318 1.159 .94 90 3370 7890 40 49 256 265 0 2922 194 2728 1.183 3331 3137 .846 1.238 .242 .308 .242
17 381 384 183 198 198 186 349 394 188 205 166 196 0 0 168 145 64 61 84 81 81 71 384 362 1.065 .939 1.181 .958 1.011 1.842 32 204 .789 .56 70 3530 7890 41 48 273 280 0 388 200 188 .949 398 198 1.054 1.193 -.076 .254 -.076
18 251 214 174 191 77 23 218 222 184 199 44 31 0 0 127 72 64 63 45 26 27 6 100 75 3.348 .299 .705 .608 .668 3.268 80 423 .223 .16 100 3670 7880 39 49 286 296 -50 216 193 23 .302 224 31 3.314 .712 -.491 -1.729
19 889 815 179 182 710 633 933 926 183 188 754 744 0 0 446 430 66 62 90 84 84 84 1343 1498 1.122 .892 .987 .816 .802 1.512 32 176 .934 .88 70 3820 7900 42 49 302 309 0 823 184 639 .901 935 752 1.11 .997 -.151 -.005 -.151
20 278 208 174 186 104 22 266 200 180 193 92 14 0 0 123 80 63 65 57 28 41 8 126 106 4.727 .212 .152 .726 .621 3.707 80 369 .383 .25 100 3960 7880 39 49 315 325 -50 210 188 22 .214 202 14 4.68 .154 -2.702 -2.227

Total number of rows: 43008

Table truncated, full table size 9432 Kbytes.




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