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Sample GSM40700 Query DataSets for GSM40700
Status Public on Jan 27, 2006
Title expression array - GBM13
Sample type RNA
 
Channel 1
Source name Cy3: Human Common Reference
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5: GBM13
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: tumor, Brain
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-10/56916
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 = 30.78; Parameter Scan Time = 18:36:15; Parameter PMT Volts = 560; Parameter Scan Date = 2004-10-05; Parameter Pixel Size = 10; Parameter Laser on time = 11003; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.44; 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 = 30.78; Parameter Scan Time = 18:36:15; Parameter PMT Volts = 660; Parameter Scan Date = 2004-10-05; Parameter Pixel Size = 10; Parameter Laser on time = 184608; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.55; 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
1 571 278 86 55 485 223 481 167 90 157 395 112 0 0 431 269 38 594 100 11 97 0 708 507 2.175 .46 .284 .25 .267 4.224 36 150 23.778 .07 70 1610 4830 63 70 37 44 0 134 26 107 .221 80 54 4.522 .136 -2.177 -2.874 -2.177
2 5894 11435 84 55 5810 11380 933 2072 90 92 849 2017 0 0 7958 14857 40 324 96 99 94 89 17190 2866 .511 1.959 2.376 2.557 2.229 2.463 133 526 1.924 .97 130 1750 4820 59 72 48 61 0 5500 26 5474 .942 997 970 1.061 1.143 -.086 .192 -.086
3 1044 859 84 53 960 806 970 665 93 68 886 612 0 0 650 696 56 70 94 94 94 91 1766 1498 1.191 .84 .691 .804 .807 2.865 36 126 .914 .7 60 1900 4830 64 70 67 73 0 413 25 388 .404 320 294 2.476 .332 -1.308 -1.59 -1.308
4 568 352 80 54 488 298 428 276 85 73 348 222 0 0 416 280 50 63 90 76 84 62 786 570 1.638 .611 .638 .532 .497 4.07 50 220 .505 .6 80 2050 4830 63 71 81 89 0 169 26 143 .294 133 107 3.405 .307 -1.767 -1.704 -1.767
5 412 147 82 56 330 91 257 80 89 74 175 24 0 0 344 139 36 69 97 33 91 25 421 199 3.626 .276 .137 .252 .199 4.581 36 176 .168 .35 70 2190 4820 62 69 95 102 0 71 27 44 .133 38 12 7.539 .066 -2.914 -3.922 -2.914
6 448 109 79 54 369 55 423 83 84 82 344 29 0 0 170 68 32 104 100 19 96 6 424 373 6.709 .149 .084 .119 .139 2.927 31 147 .138 .38 60 2340 4830 64 70 111 117 0 52 26 26 .072 40 14 13.949 .041 -3.802 -4.624 -3.802
7 860 459 86 56 774 403 304 392 87 82 218 336 0 0 2952 320 20 153 93 78 78 57 1177 554 1.921 .521 1.541 1.429 1.82 6.256 33 180 .01 .05 70 2480 4820 62 69 124 131 0 221 27 194 .25 189 162 3.993 .741 -1.997 -.432 -1.997
8 514 753 84 54 430 699 527 616 93 69 443 562 0 0 263 611 59 48 92 96 88 96 1129 1005 .615 1.626 1.269 1.725 1.185 4.61 25 144 2.539 .63 60 2630 4820 63 69 140 146 0 362 26 336 .782 296 270 1.279 .61 -.355 -.713 -.355
9 1024 1182 81 54 943 1128 815 1106 92 69 734 1052 0 0 650 677 68 78 95 97 93 95 2071 1786 .836 1.196 1.433 1.296 1.192 3.109 73 322 1.19 .74 100 2770 4820 61 71 152 162 0 569 26 543 .575 532 506 1.738 .689 -.797 -.537 -.797
10 761 475 79 54 682 421 600 356 91 82 521 302 0 0 563 347 92 114 94 86 89 63 1103 823 1.62 .617 .58 .627 .629 3.63 73 274 .402 .47 100 2920 4820 61 71 167 177 0 228 26 202 .297 171 145 3.368 .279 -1.752 -1.843 -1.752
11 3707 3735 79 56 3628 3679 3610 3834 87 93 3531 3778 0 0 2327 1878 98 164 93 100 92 98 7307 7309 .986 1.014 1.07 1.288 1.163 2.766 77 263 .927 .84 100 3070 4820 61 71 182 192 0 1796 27 1770 .488 1844 1817 2.05 .515 -1.036 -.958 -1.036
12 9955 22353 79 55 9876 22298 11150 26843 88 95 11071 26788 0 0 8467 17661 83 229 97 100 94 95 32174 37859 .443 2.258 2.42 2.757 2.24 2.501 106 408 2.209 .97 120 3210 4820 60 72 195 207 0 10752 26 10725 1.086 12911 12885 .921 1.164 .119 .219 .119
13 1481 3713 79 53 1402 3660 1389 3761 92 73 1310 3708 0 0 1013 1615 56 68 93 100 90 100 5062 5018 .383 2.611 2.831 3.676 2.789 3.055 75 215 2.679 .76 90 3360 4810 60 69 211 220 0 1786 25 1760 1.256 1809 1784 .796 1.361 .328 .445 .328
14 215 1177 78 56 137 1121 116 1044 89 68 38 988 0 0 243 667 51 53 47 100 33 100 1258 1026 .122 8.182 26 13.041 16.09 4.314 84 305 12.765 .31 100 3500 4820 61 71 225 235 0 566 27 539 3.936 502 475 .254 12.506 1.977 3.645 1.977
15 378 1807 80 58 298 1749 312 1289 86 85 232 1231 0 0 261 1896 36 94 84 100 78 100 2047 1463 .17 5.869 5.306 7.541 6.007 3.732 64 203 13.848 .47 90 3650 4820 61 70 240 249 0 869 28 841 2.823 620 592 .354 2.552 1.497 1.352 1.497
16 28950 30365 80 56 28870 30309 13120 17418 87 82 13040 17362 17 18 28239 27979 38 107 99 100 99 100 59179 30402 .953 1.05 1.331 1.182 1 1.803 129 370 1.015 .98 120 3800 4820 60 72 254 266 0 14605 27 14578 .505 8378 8351 1.98 .64 -.986 -.643 -.986
17 3175 3753 79 55 3096 3698 3124 3983 83 69 3045 3928 0 0 1827 2132 30 65 100 100 97 100 6794 6973 .837 1.194 1.29 1.282 1.142 2.313 76 247 1.208 .88 100 3950 4820 61 71 270 280 0 1805 26 1779 .575 1916 1889 1.741 .62 -.8 -.689 -.8
18 526 1490 78 54 448 1436 442 1434 116 74 364 1380 0 0 431 596 527 82 30 100 9 100 1884 1744 .312 3.205 3.791 4.817 4.034 3.935 76 236 3.749 .54 100 4080 4820 61 71 283 293 0 717 26 691 1.542 690 664 .649 1.824 .625 .867 .625
19 2771 5516 77 54 2694 5462 2788 6385 111 98 2711 6331 0 0 1739 2951 478 255 83 100 78 97 8156 9042 .493 2.027 2.335 2.58 2.174 2.505 85 286 2.022 .91 110 4240 4820 60 71 298 309 0 2653 26 2627 .975 3071 3045 1.025 1.123 -.036 .168 -.036
20 2201 4277 79 56 2122 4221 2262 4322 90 101 2183 4266 0 0 1543 2467 49 264 97 100 95 100 6343 6449 .503 1.989 1.954 2.662 2.041 2.81 88 258 1.986 .86 100 4380 4820 61 71 313 323 0 2057 27 2030 .957 2079 2052 1.045 .94 -.064 -.089 -.064

Total number of rows: 41472

Table truncated, full table size 9348 Kbytes.




Supplementary data files not provided
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