NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM39919 Query DataSets for GSM39919
Status Public on Feb 21, 2005
Title Cervix, endo cervical canal 1200
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Cervix, endo cervical canal 1200
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-11/21898.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
1 548 1113 196 178 352 935 535 1169 199 192 339 991 0 0 219 462 61 84 86 90 80 88 1287 1330 .376 2.656 2.923 2.721 2.573 2.023 52 294 2.828 .82 80 1310 7480 48 56 51 59 0 959 153 806 2.29 1008 854 .437 2.52 1.195 1.333 1.195
2 413 226 200 167 213 59 451 230 210 183 251 63 0 0 159 94 72 87 84 37 78 15 272 314 3.61 .277 .251 .385 .397 1.908 32 224 .357 .29 70 1450 7490 49 56 65 72 0 195 144 51 .239 198 54 4.188 .216 -2.066 -2.208 -2.066
3 1302 1239 197 183 1105 1056 1396 1384 203 189 1199 1201 0 0 610 554 68 80 90 94 88 90 2161 2400 1.046 .956 1.002 .858 .925 2.102 52 292 .941 .91 80 1610 7480 48 56 81 89 0 1068 158 910 .824 1193 1035 1.214 .864 -.28 -.212 -.28
4 4741 5652 206 186 4535 5466 4601 5484 208 198 4395 5298 0 0 2567 3051 66 78 100 100 100 100 10001 9693 .83 1.205 1.205 1.197 1.129 1.67 52 246 1.208 .96 80 1750 7480 48 56 95 103 0 4872 160 4712 1.039 4728 4567 .962 1.039 .055 .055 .055
5 593 703 218 208 375 495 651 662 222 215 433 454 0 0 251 342 71 82 88 84 78 82 870 887 .758 1.32 1.048 1.231 1.377 2.445 52 302 1.417 .81 80 1900 7480 48 56 110 118 0 606 179 427 1.138 571 391 .879 .904 .186 -.146 .186
6 423 380 239 197 184 183 407 393 247 205 168 196 0 0 96 119 78 74 91 75 50 58 367 364 1.005 .995 1.167 1.058 .982 2.213 12 104 1.011 .43 50 2050 7490 50 55 126 131 -100 328 170 158 .857 339 169 1.166 1.006 .008 -.222
7 727 937 205 205 522 732 777 988 219 219 572 783 0 0 261 367 100 97 88 90 88 88 1254 1355 .713 1.402 1.369 1.377 1.346 1.45 52 268 1.437 .85 80 2190 7480 48 56 139 147 0 808 177 631 1.209 852 675 .827 1.18 .274 .239 .274
8 4993 7926 199 232 4794 7694 5282 8174 213 232 5083 7942 0 0 2651 4121 93 94 96 100 94 100 12488 13025 .623 1.605 1.562 1.74 1.664 1.746 52 316 1.6 .97 90 2340 7480 47 56 153 162 0 6833 200 6633 1.384 7047 6847 .723 1.347 .468 .43 .468
9 1201 1568 199 226 1002 1342 1311 1663 212 234 1112 1437 0 0 484 599 83 88 93 96 90 96 2344 2549 .747 1.339 1.292 1.384 1.333 1.876 32 220 1.287 .92 70 2480 7480 48 55 168 175 0 1352 195 1157 1.155 1434 1239 .866 1.114 .207 .156 .207
10 423 340 190 190 233 150 446 367 203 205 256 177 0 0 113 137 83 84 87 68 81 53 383 433 1.553 .644 .691 .598 .717 2.347 32 228 .824 .48 70 2620 7480 48 55 182 189 0 293 164 129 .555 316 153 1.802 .596 -.849 -.747 -.849
11 1085 1274 182 203 903 1071 1191 1482 188 216 1009 1279 0 0 590 631 53 83 87 93 87 93 1974 2288 .843 1.186 1.268 1.239 1.1 1.662 32 218 1.135 .93 70 2770 7480 48 55 197 204 0 1098 175 923 1.022 1278 1103 .978 1.093 .032 .128 .032
12 1282 1591 185 231 1097 1360 1316 1614 190 239 1131 1383 0 0 576 687 62 90 96 96 94 94 2457 2514 .807 1.24 1.223 1.289 1.216 1.868 52 268 1.229 .9 80 2920 7480 48 56 212 220 0 1372 199 1172 1.069 1391 1192 .936 1.054 .096 .076 .096
13 947 1092 185 219 762 873 1076 1268 190 228 891 1049 0 0 350 429 63 82 93 90 93 84 1635 1940 .873 1.146 1.177 1.345 1.19 1.976 32 212 1.172 .9 70 3060 7480 48 55 226 233 0 941 189 753 .988 1093 904 1.013 1.015 -.018 .021 -.018
14 373 1060 181 211 192 849 423 1106 192 220 242 895 0 0 152 453 58 83 81 90 68 87 1041 1137 .226 4.422 3.698 3.259 4.566 3.29 32 224 4.701 .72 70 3210 7480 48 55 241 248 0 914 182 732 3.812 953 772 .262 3.188 1.931 1.673 1.931
15 5601 5780 181 211 5420 5569 5749 6424 190 216 5568 6213 0 0 2175 2807 61 79 98 100 98 100 10989 11781 .973 1.027 1.116 .893 1.048 2.062 52 309 1.093 .95 90 3350 7470 46 55 254 263 0 4983 182 4801 .886 5538 5356 1.129 .962 -.175 -.056 -.175
16 1735 2350 180 214 1555 2136 1886 2506 187 219 1706 2292 0 0 634 784 62 82 98 98 98 98 3691 3998 .728 1.374 1.343 1.396 1.33 2.399 52 330 1.387 .94 90 3500 7480 47 56 269 278 0 2026 184 1841 1.184 2160 1976 .844 1.158 .244 .212 .244
17 312 318 190 207 122 111 319 306 194 219 129 99 0 0 133 141 64 86 75 50 50 34 233 228 1.099 .91 .767 1.028 1.105 2.5 32 164 1.324 .38 60 3650 7480 49 55 286 292 0 274 178 96 .784 264 85 1.275 .662 -.35 -.596 -.35
18 243 240 196 209 47 31 225 227 202 226 29 18 0 0 109 97 66 92 40 27 21 7 78 47 1.516 .66 .621 .822 .77 4.602 80 446 2.055 .15 100 3790 7470 46 56 298 308 -50 207 180 27 .569 196 16 1.759 .535 -.902 -.815
19 872 1040 196 206 676 834 920 980 205 219 724 774 0 0 450 479 65 86 84 90 81 87 1510 1498 .811 1.234 1.069 1.363 1.219 2.296 32 195 1.177 .9 70 3940 7490 49 56 314 321 0 897 178 719 1.064 845 667 .94 .922 .089 -.118 .089
20 360 314 190 184 170 130 351 305 195 196 161 121 0 0 125 111 62 88 81 59 56 31 300 282 1.308 .765 .752 .751 .722 3.703 32 207 .676 .33 70 4100 7470 47 54 330 337 0 271 159 112 .659 263 104 1.517 .648 -.601 -.626 -.601

Total number of rows: 43008

Table truncated, full table size 9361 Kbytes.




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