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Sample GSM40665 Query DataSets for GSM40665
Status Public on Jan 27, 2006
Title expression array - JPA2
Sample type RNA
 
Channel 1
Source name Cy3: Human Common Reference
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5: JPA2
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: tumor, Brain
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-09/55549
Sample_scan_protocol: 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 = 29.65; Parameter Scan Time = 17:43:11; Parameter PMT Volts = 560; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 6488; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.48; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
Sample_scan_protocol: 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 = 29.65; Parameter Scan Time = 17:43:11; Parameter PMT Volts = 660; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 180030; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.52; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
 
Submission date Feb 01, 2005
Last update date Mar 22, 2006
Contact name Markus Bredel
E-mail(s) mbredel@stanford.edu
Phone 650-498-6012
Organization name Stanford University School of Medicine
Street address
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL1833
Series (1)
GSE2223 Gene expression profiling in human glial brain tumors

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
1 280 624 76 53 204 571 230 491 90 59 154 438 0 0 176 551 48 31 90 95 79 93 775 592 .357 2.799 2.844 2.454 2.898 3.197 44 253 5.383 .5 80 1920 5350 53 61 67 75 0 309 26 283 1.387 243 217 .721 1.41 .472 .495 .472
2 8824 2647 77 51 8747 2596 3917 1658 94 59 3840 1607 0 0 8839 2561 54 51 98 92 97 85 11343 5447 3.369 .297 .418 .337 .308 2.874 77 345 .281 .95 100 2060 5350 52 62 80 90 0 1312 25 1287 .147 822 797 6.798 .207 -2.765 -2.269 -2.765
3 637 745 78 50 559 695 453 409 92 61 375 359 0 0 504 727 45 35 91 97 91 94 1254 734 .804 1.243 .957 1.071 .874 3.536 36 128 1.579 .65 60 2210 5360 55 61 97 103 0 369 25 344 .616 203 178 1.623 .475 -.698 -1.076 -.698
4 560 375 77 54 483 321 417 291 96 63 340 237 0 0 362 311 67 37 97 85 95 77 804 577 1.505 .665 .697 .634 .597 2.844 40 189 .677 .7 70 2360 5350 53 60 111 118 0 186 27 159 .329 144 117 3.036 .345 -1.602 -1.533 -1.602
5 383 181 80 55 303 126 220 76 102 60 140 21 0 0 355 297 73 24 73 46 46 36 429 161 2.405 .416 .15 .191 .218 5.767 30 127 1.139 .05 60 2510 5350 54 60 127 133 0 90 27 62 .206 38 10 4.852 .074 -2.278 -3.75 -2.278
6 289 163 77 52 212 111 222 80 97 68 145 28 0 0 237 160 68 53 83 43 54 37 323 173 1.91 .524 .193 .332 .467 4.289 37 248 .452 .54 80 2640 5350 53 61 139 147 0 81 26 55 .26 40 14 3.853 .096 -1.946 -3.385 -1.946
7 312 395 76 53 236 342 266 193 91 68 190 140 0 0 217 498 53 59 87 60 72 54 578 330 .69 1.449 .737 .727 1.063 7.632 33 188 3.57 .42 70 2780 5350 53 60 153 160 0 196 26 170 .718 96 69 1.392 .365 -.477 -1.453 -.477
8 313 625 73 56 240 569 243 367 81 70 170 311 0 0 198 630 33 48 90 86 73 76 809 481 .422 2.371 1.829 1.955 2.389 3.209 30 152 3.35 .79 60 2940 5350 54 60 170 176 0 310 28 282 1.175 182 154 .851 .907 .233 -.141 .233
9 1013 1214 76 54 937 1160 835 1147 90 64 759 1093 0 0 1057 590 49 37 96 100 95 100 2097 1852 .808 1.238 1.44 1.426 1.577 2.382 61 218 .758 .54 80 3090 5350 53 61 184 192 0 602 27 575 .614 569 542 1.63 .714 -.705 -.486 -.705
10 488 290 76 56 412 234 409 230 85 72 333 174 0 0 525 226 38 60 85 72 81 62 646 507 1.761 .568 .523 .714 .719 7.049 54 218 .09 .14 90 3230 5350 52 61 197 206 0 144 28 116 .282 114 86 3.552 .259 -1.829 -1.949 -1.829
11 2730 3563 78 56 2652 3507 2902 3795 99 72 2824 3739 0 0 1646 2001 96 59 94 98 89 98 6159 6563 .756 1.322 1.324 1.513 1.468 2.89 76 291 1.331 .88 100 3380 5350 52 62 212 222 0 1766 28 1738 .655 1881 1853 1.526 .656 -.609 -.608 -.609
12 5702 18589 80 56 5622 18533 5470 17175 107 65 5390 17119 0 0 4987 15933 96 42 92 100 85 100 24155 22509 .303 3.297 3.176 3.526 3.266 2.414 99 300 3.36 .96 110 3530 5350 51 62 226 237 0 9214 28 9186 1.634 8513 8485 .612 1.574 .708 .655 .708
13 1149 3914 83 54 1066 3860 1048 3995 116 70 965 3941 0 0 674 1814 111 52 93 100 87 100 4926 4906 .276 3.621 4.084 4.073 3.59 2.062 66 211 3.978 .8 90 3670 5350 52 61 241 250 0 1940 27 1913 1.795 1980 1953 .557 2.024 .844 1.017 .844
14 191 918 80 52 111 866 119 807 99 64 39 755 0 0 193 465 70 40 38 98 28 97 977 794 .128 7.802 19.359 15.599 10.995 6.526 75 300 13.599 .25 100 3810 5350 52 62 255 265 0 455 26 429 3.867 400 374 .259 9.595 1.951 3.262 1.951
15 251 1793 79 55 172 1738 137 1722 104 69 58 1667 0 0 283 852 81 48 39 100 27 98 1910 1725 .099 10.105 28.741 20.353 21.716 7.183 68 196 22.331 .22 90 3960 5350 52 61 270 279 0 889 27 861 5.008 854 826 .2 14.246 2.324 3.832 2.324
16 26511 21231 78 59 26433 21172 18241 14862 96 76 18163 14803 0 0 25543 20595 72 65 98 100 98 99 47605 32966 1.248 .801 .815 .917 .81 1.973 118 395 .801 .98 120 4110 5350 51 63 284 296 0 10523 29 10494 .397 7366 7337 2.519 .404 -1.333 -1.308 -1.333
17 1738 5020 77 56 1661 4964 1772 5434 90 69 1695 5378 0 0 906 2339 71 56 98 100 94 100 6625 7073 .335 2.989 3.173 3.215 3.005 1.722 67 213 3.149 .89 90 4250 5340 51 60 299 308 0 2488 28 2460 1.481 2693 2666 .675 1.573 .567 .653 .567
18 386 989 82 54 304 935 335 901 108 66 253 847 0 0 247 378 133 35 73 100 45 100 1239 1100 .325 3.076 3.348 4.082 3.324 3.062 60 181 3.389 .65 80 4400 5350 53 61 315 323 0 490 27 463 1.524 447 420 .656 1.659 .608 .731 .608
19 2333 2554 85 56 2248 2498 2257 2377 121 66 2172 2321 0 0 1410 1351 144 35 96 100 95 100 4746 4493 .9 1.111 1.069 1.101 1.082 1.87 66 206 1.073 .84 80 4540 5340 52 60 329 337 0 1266 28 1238 .551 1178 1150 1.816 .53 -.86 -.917 -.86
20 1456 1829 82 56 1374 1773 1262 1907 112 65 1180 1851 0 0 1037 918 97 38 98 100 92 100 3147 3031 .775 1.29 1.569 1.561 1.408 2.427 66 238 1.159 .81 90 4690 5350 52 61 343 352 0 907 28 879 .64 945 917 1.564 .778 -.645 -.363 -.645

Total number of rows: 41472

Table truncated, full table size 9307 Kbytes.




Supplementary data files not provided
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