NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM39971 Query DataSets for GSM39971
Status Public on Feb 21, 2005
Title Spleen 0125
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Spleen 0125
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://jdemeter-smd.stanford.edu:8000/MicroArray/gifs/2001-03/14624.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 GPL1825
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
1 719 614 167 144 552 470 789 693 172 155 622 549 0 0 247 260 44 63 92 86 92 82 1022 1171 1.174 .851 .883 .846 .872 1.782 80 369 .868 .88 100 1120 8340 73 83 55 65 0 590 138 452 .819 666 528 1.221 .849 -.289 -.237 -.289
2 888 859 166 138 722 721 830 803 166 143 664 665 0 0 504 538 38 55 100 93 96 90 1443 1329 1.001 .999 1.002 .898 .844 2.423 32 83 1.036 .83 60 1280 8350 76 82 73 79 -100 826 133 693 .96 772 639 1.041 .963 -.054 -.059
3 2861 2071 168 138 2693 1933 3025 2170 171 144 2857 2032 0 0 682 628 39 54 100 100 100 100 4626 4889 1.393 .718 .711 .691 .714 1.433 80 247 .722 .91 100 1400 8340 73 83 83 93 0 1991 133 1859 .69 2087 1954 1.449 .684 -.535 -.548 -.535
4 947 838 166 140 781 698 836 847 173 146 670 707 0 0 626 570 39 52 93 81 87 75 1479 1377 1.119 .894 1.055 .894 .905 3.292 32 113 .87 .77 70 1540 8350 75 82 98 105 -100 806 135 671 .859 814 680 1.164 1.015 .021 -.219
5 1018 1059 173 151 845 908 964 1078 188 158 791 927 0 0 234 291 139 82 100 97 100 96 1753 1718 .931 1.075 1.172 1.052 1.128 1.668 80 274 1.225 .84 100 1670 8340 73 83 110 120 0 1018 145 873 1.033 1037 891 .968 1.127 .047 .172 .047
6 727 589 185 155 542 434 768 592 187 161 583 437 0 0 358 389 46 66 87 71 78 62 976 1020 1.249 .801 .75 .752 .773 2.386 32 88 .883 .84 60 1800 8350 76 82 125 131 -100 566 149 417 .77 569 420 1.299 .721 -.472 -.377
7 853 971 203 164 650 807 844 992 206 173 641 828 0 0 175 320 47 71 100 95 100 93 1457 1469 .805 1.242 1.292 1.102 1.271 1.937 80 244 1.37 .89 100 1940 8340 73 83 137 147 0 934 158 776 1.194 954 796 .838 1.242 .256 .313 .256
8 1135 1059 199 174 936 885 1101 993 207 189 902 819 0 0 274 379 56 77 100 100 100 100 1821 1721 1.058 .946 .908 .899 .95 1.399 80 214 .993 .88 100 2080 8340 73 83 151 161 0 1018 167 851 .909 955 788 1.1 .873 -.137 -.196 -.137
9 530 416 187 165 343 251 505 365 195 177 318 200 0 0 243 225 55 70 86 75 86 59 594 518 1.367 .732 .629 .622 .707 3.009 52 214 .807 .71 80 2200 8290 69 77 164 172 0 400 159 241 .704 351 192 1.421 .605 -.507 -.726 -.507
10 444 540 168 149 276 391 432 517 172 157 264 368 0 0 106 172 40 62 100 98 98 93 667 632 .706 1.417 1.394 1.405 1.432 1.913 80 252 1.665 .71 100 2340 8320 71 81 177 187 0 519 143 376 1.362 497 354 .734 1.34 .446 .423 .446
11 1896 1383 167 151 1729 1232 2015 1462 171 157 1848 1311 0 0 458 497 41 63 100 98 100 96 2961 3159 1.403 .713 .709 .64 .719 1.799 80 278 .736 .91 100 2470 8300 69 79 190 200 0 1330 145 1185 .685 1406 1261 1.46 .682 -.546 -.552 -.546
12 780 813 172 158 608 655 758 838 179 165 586 680 0 0 241 244 45 65 100 100 98 100 1263 1266 .928 1.077 1.16 1.093 1.097 1.689 52 227 1.076 .83 90 2610 8310 70 79 204 213 0 782 152 630 1.036 806 654 .965 1.116 .051 .158 .051
13 600 555 180 163 420 392 589 535 185 172 409 372 0 0 151 224 43 67 100 91 98 88 812 781 1.071 .933 .91 .851 .967 1.936 80 273 1.07 .84 100 2750 8310 70 80 218 228 0 534 157 377 .897 514 358 1.114 .875 -.156 -.193 -.156
14 710 847 184 167 526 680 706 858 187 174 522 691 0 0 179 207 38 65 100 100 100 98 1206 1213 .774 1.293 1.324 1.312 1.321 1.565 80 247 1.331 .87 110 2890 8320 70 81 231 242 0 814 161 654 1.243 825 664 .804 1.273 .314 .348 .314
15 813 857 179 169 634 688 791 853 184 175 612 684 0 0 362 397 44 67 100 96 97 92 1322 1296 .922 1.085 1.118 1.031 1.179 2.389 80 260 1.12 .85 100 3030 8300 69 79 246 256 0 824 163 662 1.043 820 658 .958 1.075 .061 .104 .061
16 1436 1820 181 166 1255 1654 1468 1814 187 178 1287 1648 0 0 264 387 47 73 100 100 100 100 2909 2935 .759 1.318 1.28 1.308 1.287 1.337 80 297 1.353 .89 110 3150 8300 68 79 257 268 0 1750 160 1590 1.267 1744 1585 .789 1.231 .342 .3 .342
17 715 950 178 177 537 773 728 939 185 181 550 762 0 0 188 286 44 72 100 100 100 100 1310 1312 .695 1.439 1.385 1.45 1.402 1.602 80 256 1.5 .84 100 3280 8310 70 80 271 281 0 913 170 743 1.384 903 733 .722 1.332 .469 .414 .469
18 493 330 183 175 310 155 491 315 186 178 308 140 0 0 102 118 42 62 98 85 97 57 465 448 2 .5 .455 .468 .467 2.089 80 315 .618 .65 110 3430 8300 68 79 285 296 0 317 168 149 .481 303 135 2.08 .437 -1.057 -1.194 -1.057
19 525 582 187 177 338 405 515 563 189 182 328 386 0 0 132 173 41 65 98 98 97 95 743 714 .835 1.198 1.177 1.19 1.297 1.633 80 239 1.295 .81 100 3550 8310 70 80 298 308 0 560 170 389 1.152 541 371 .868 1.132 .204 .178 .204
20 1467 1215 196 188 1271 1027 1433 1322 196 191 1237 1134 0 0 348 425 43 69 100 96 100 93 2298 2371 1.238 .808 .917 .698 .817 1.874 80 293 .858 .91 110 3690 8310 69 80 311 322 0 1168 181 988 .777 1271 1090 1.287 .881 -.364 -.182 -.364

Total number of rows: 44160

Table truncated, full table size 9913 Kbytes.




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