NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM39999 Query DataSets for GSM39999
Status Public on Feb 21, 2005
Title Heart 0841
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Heart 0841
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-12/36427.gif
Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.99; Parameter Scan Time = 10:26:45; Parameter PMT Volts = 625; Parameter Scan Date = 2002-12-14; Parameter Pixel Size = 10; Parameter Laser on time = 45087; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 4.83; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Radha,,Shyamsundar
Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.99; Parameter Scan Time = 10:26:45; Parameter PMT Volts = 750; Parameter Scan Date = 2002-12-14; Parameter Pixel Size = 10; Parameter Laser on time = 264082; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.08; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Radha,,Shyamsundar
 
Submission date Jan 26, 2005
Last update date Nov 22, 2005
Contact name Jonathan Pollack
E-mail(s) [email protected]
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 GPL1826
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
1 303 420 139 125 164 295 294 269 142 137 155 144 0 0 169 751 32 59 88 82 80 67 459 299 .556 1.799 .929 1.11 1.03 2.923 52 254 3.272 .36 80 1670 8470 59 67 79 87 0 444 132 312 1.903 285 152 .525 .983 .929 -.025 .929
2 408 548 141 136 267 412 413 536 147 161 272 400 0 0 131 189 44 225 92 86 90 36 679 672 .648 1.543 1.471 1.55 1.42 1.972 52 255 1.697 .74 80 1820 8460 58 66 94 102 0 580 144 436 1.633 567 423 .612 1.556 .707 .638 .707
3 641 573 141 143 500 430 670 581 147 217 529 438 0 0 224 169 50 475 93 40 93 0 930 967 1.163 .86 .828 .988 .782 3.09 32 199 6.238 .24 70 1960 8460 58 65 108 115 0 606 151 455 .91 615 463 1.099 .876 -.136 -.191 -.136
4 242 297 143 145 99 152 190 200 149 206 47 55 0 0 146 692 41 640 53 2 41 1 251 102 .651 1.535 1.17 .956 .996 3.01 80 364 21.906 .53 100 2120 8470 58 68 123 133 0 314 153 161 1.625 212 58 .616 1.238 .7 .308 .7
5 537 1001 145 145 392 856 551 983 151 227 406 838 0 0 138 340 48 722 100 65 96 7 1248 1244 .458 2.184 2.064 2.129 2.336 1.842 52 287 2.438 .83 90 2240 8450 56 65 135 144 0 1059 153 906 2.311 1040 887 .433 2.184 1.208 1.127 1.208
6 295 278 146 145 149 133 301 276 145 155 155 131 0 0 61 86 27 70 100 75 96 46 282 286 1.12 .893 .845 .737 .96 3.486 32 212 1.648 .43 70 2400 8450 57 64 152 159 0 294 153 141 .945 292 139 1.059 .894 -.082 -.161 -.082
7 490 494 142 142 348 352 510 522 143 148 368 380 0 0 197 169 29 58 94 96 88 92 700 748 .989 1.011 1.033 1.174 .988 2.786 52 316 .955 .72 90 2540 8460 57 66 165 174 0 523 150 372 1.07 552 402 .934 1.093 .098 .128 .098
8 390 333 144 146 246 187 390 334 148 159 246 188 0 0 90 109 35 73 98 82 96 69 433 434 1.316 .76 .764 .613 .697 2.483 52 275 .895 .69 80 2690 8450 57 65 181 189 0 352 154 198 .804 353 199 1.243 .809 -.314 -.306 -.314
9 356 414 143 148 213 266 366 406 146 154 223 258 0 0 70 131 31 64 98 98 98 84 479 481 .801 1.249 1.157 1.055 1.136 2.294 52 322 1.625 .68 90 2830 8450 56 65 194 203 0 438 157 281 1.321 430 273 .757 1.224 .402 .292 .402
10 269 252 142 144 127 108 270 236 144 162 128 92 0 0 73 92 34 122 86 40 76 5 235 220 1.176 .85 .719 .881 .743 2.282 52 251 45.983 .22 80 2990 8450 57 65 211 219 0 267 152 114 .9 250 97 1.111 .761 -.152 -.395 -.152
11 660 1014 140 144 520 870 704 1041 143 158 564 897 0 0 243 335 33 108 96 100 92 96 1390 1461 .598 1.673 1.59 1.81 1.578 2.392 80 353 1.765 .82 100 3130 8460 57 67 224 234 0 1073 152 921 1.77 1102 949 .565 1.683 .824 .751 .824
12 2109 1688 139 144 1970 1544 2011 1677 143 152 1872 1533 0 0 1143 998 29 65 98 96 94 94 3514 3405 1.276 .784 .819 .847 .735 2.846 52 244 .771 .86 80 3280 8450 57 65 240 248 0 1786 152 1634 .829 1775 1622 1.206 .867 -.27 -.207 -.27
13 353 727 147 143 206 584 355 757 149 149 208 614 0 0 86 188 31 64 98 100 96 98 790 822 .353 2.835 2.952 2.902 2.84 1.79 52 312 3.119 .77 90 3420 8450 56 65 253 262 0 769 151 618 3 801 650 .333 3.124 1.585 1.643 1.585
14 329 348 146 151 183 197 324 343 158 170 178 192 0 0 75 97 101 199 86 46 42 1 380 370 .929 1.077 1.079 1.035 .974 1.701 52 289 1.432 .68 90 3570 8460 57 66 268 277 0 368 160 208 1.139 363 203 .878 1.141 .188 .191 .188
15 511 1424 151 149 360 1275 555 1450 164 168 404 1301 0 0 167 363 100 191 88 100 82 97 1635 1705 .282 3.542 3.22 3.582 3.372 1.655 80 319 3.661 .88 100 3710 8460 57 67 282 292 0 1507 158 1349 3.748 1534 1377 .267 3.408 1.906 1.769 1.906
16 2648 3165 151 132 2497 3033 2872 3421 152 141 2721 3289 0 0 1212 1215 30 57 98 100 97 100 5530 6010 .823 1.215 1.209 1.456 1.189 2.356 80 325 1.171 .92 100 3860 8460 57 67 297 307 0 3349 140 3209 1.285 3620 3480 .778 1.279 .362 .355 .362
17 472 874 144 132 328 742 471 886 148 171 327 754 0 0 123 322 55 448 98 82 98 32 1070 1081 .442 2.262 2.306 2.051 2.25 1.627 52 233 2.47 .87 80 4000 8450 57 65 312 320 0 925 140 785 2.394 938 798 .418 2.44 1.259 1.287 1.259
18 160 190 141 135 19 55 143 163 360 654 2 28 0 0 54 92 1606 3946 0 0 0 0 74 30 .345 2.895 14 2.463 2.495 4.123 52 246 3.127 .85 80 4140 8440 56 64 326 334 -50 201 143 58 3.063 172 30 .326 14.814 3.889 1.615
19 1040 733 142 136 898 597 1117 736 145 147 975 600 0 0 378 305 30 58 100 96 98 92 1495 1575 1.504 .665 .615 .67 .655 2.036 80 365 .687 .84 100 4290 8450 56 66 340 350 0 776 144 632 .703 779 635 1.422 .651 -.507 -.619 -.507
20 691 581 148 153 543 428 702 566 151 158 554 413 0 0 194 171 36 63 96 100 96 98 971 967 1.269 .788 .745 .802 .811 2.071 52 254 .827 .81 80 4430 8450 57 65 355 363 0 615 162 453 .834 599 437 1.199 .789 -.262 -.342 -.262

Total number of rows: 43104

Table truncated, full table size 9406 Kbytes.




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