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Sample GSM40676 Query DataSets for GSM40676
Status Public on Jan 27, 2006
Title expression array - GBM15
Sample type RNA
 
Channel 1
Source name Cy3: Human Common Reference
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5: GBM15
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: tumor, Brain
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-10/56923
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 = 31.64; Parameter Scan Time = 20:38:09; Parameter PMT Volts = 570; Parameter Scan Date = 2004-10-08; Parameter Pixel Size = 10; Parameter Laser on time = 12086; 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 = 31.64; Parameter Scan Time = 20:38:09; Parameter PMT Volts = 660; Parameter Scan Date = 2004-10-08; Parameter Pixel Size = 10; Parameter Laser on time = 185691; 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
1 499 581 119 53 380 528 427 488 124 63 308 435 0 0 216 417 39 68 100 97 100 86 908 743 .72 1.389 1.412 1.317 1.262 2.543 38 168 2.266 .53 70 1810 5150 55 62 61 68 0 371 34 337 .887 311 278 1.127 .902 -.173 -.15 -.173
2 4849 1863 121 53 4728 1810 1337 645 129 66 1216 592 0 0 5344 2328 59 70 98 83 94 74 6538 1808 2.612 .383 .487 .332 .325 3.532 104 485 .389 .91 120 1950 5160 54 66 73 85 0 1189 34 1155 .244 412 378 4.092 .311 -2.033 -1.686 -2.033
3 1339 1055 114 60 1225 995 1094 932 119 75 980 872 0 0 899 598 33 63 100 95 100 91 2220 1852 1.231 .812 .89 .776 .847 2.358 24 67 .711 .79 50 2090 5160 57 62 90 95 0 673 38 635 .518 595 557 1.929 .568 -.948 -.816 -.948
4 749 301 118 53 631 248 702 160 122 75 584 107 0 0 540 514 35 182 92 38 84 20 879 691 2.544 .393 .183 .206 .274 7.61 39 291 .436 .36 80 2250 5150 55 63 105 113 0 192 34 158 .251 102 68 3.986 .117 -1.995 -3.096 -1.995
5 433 228 119 57 314 171 307 101 136 84 188 44 0 0 479 273 79 244 75 21 57 15 485 232 1.836 .545 .234 .422 .373 7.939 33 144 .196 .25 60 2400 5160 57 63 121 127 0 146 36 109 .348 64 28 2.877 .149 -1.524 -2.743 -1.524
6 651 239 115 53 536 186 530 124 118 58 415 71 0 0 326 246 41 18 100 85 100 70 722 486 2.882 .347 .171 .17 .166 4.851 27 149 .27 .4 60 2530 5160 57 63 134 140 0 153 34 119 .222 79 45 4.515 .109 -2.175 -3.195 -2.175
7 516 385 123 59 393 326 376 313 129 74 253 254 0 0 369 235 51 89 89 89 82 67 719 507 1.206 .83 1.004 1.004 1.115 4.564 28 203 .433 .43 70 2690 5160 56 63 149 156 0 246 38 208 .529 200 162 1.889 .641 -.917 -.642 -.917
8 595 1263 117 59 478 1204 491 827 126 70 374 768 0 0 345 1008 43 42 93 96 90 93 1682 1142 .397 2.519 2.053 1.873 2.354 3.832 30 131 4.112 .6 60 2840 5160 57 63 165 171 0 806 38 769 1.608 528 490 .622 1.311 .685 .39 .685
9 1181 1384 116 54 1065 1330 1053 1321 127 64 937 1267 0 0 681 729 62 43 95 100 95 98 2395 2204 .801 1.249 1.352 1.286 1.116 2.911 64 239 1.26 .72 90 2970 5150 54 63 176 185 0 883 34 849 .797 843 809 1.254 .863 -.327 -.212 -.327
10 651 253 116 56 535 197 504 197 131 63 388 141 0 0 545 261 87 31 84 78 79 65 732 529 2.716 .368 .363 .356 .381 6.413 73 278 .181 .34 100 3110 5150 54 64 190 200 0 161 36 126 .235 126 90 4.255 .232 -2.089 -2.108 -2.089
11 2978 3652 117 57 2861 3595 3181 4012 130 63 3064 3955 0 0 1861 2162 79 36 92 100 91 98 6456 7019 .796 1.257 1.291 1.286 1.221 2.553 82 321 1.241 .93 110 3260 5150 53 64 204 215 0 2331 36 2295 .802 2561 2525 1.247 .824 -.318 -.279 -.318
12 8066 21799 117 58 7949 21741 8299 26968 126 67 8182 26910 0 0 6581 16413 67 52 93 98 92 98 29690 35092 .366 2.735 3.289 3.218 2.69 3.073 91 332 2.75 .94 110 3400 5150 53 64 218 229 0 13915 37 13878 1.746 17214 17177 .573 2.099 .804 1.07 .804
13 1389 5233 118 56 1271 5177 1257 5477 127 65 1139 5421 0 0 1083 2618 50 45 93 100 93 100 6448 6560 .246 4.073 4.759 4.731 4.712 2.448 66 223 4.138 .78 90 3550 5150 54 63 234 243 0 3340 36 3305 2.6 3496 3460 .385 3.038 1.378 1.603 1.378
14 298 1891 117 56 181 1835 184 1720 122 140 67 1664 0 0 293 1299 43 1040 51 77 45 30 2016 1731 .099 10.138 24.836 12.043 8.895 5.766 80 358 19.938 .3 110 3690 5140 52 63 247 258 0 1207 36 1171 6.471 1098 1062 .155 15.853 2.694 3.987 2.694
15 374 11365 118 58 256 11307 276 12322 124 178 158 12264 0 0 343 6054 46 1210 66 92 55 88 11563 12422 .023 44.168 77.62 72.104 60.816 3.965 84 268 47.411 .58 100 3840 5150 54 64 263 273 0 7254 37 7217 28.193 7865 7828 .035 49.546 4.817 5.631 4.817
16 31341 26821 118 57 31223 26764 27810 29070 126 148 27692 29013 7 0 25297 21163 52 736 100 96 100 92 57987 56705 1.167 .857 1.048 .869 .865 1.817 98 298 .843 .97 110 3990 5150 53 64 277 288 0 17120 36 17084 .547 18556 18520 1.828 .669 -.87 -.58 -.87
17 1724 4450 117 58 1607 4392 1461 3978 125 78 1344 3920 0 0 1353 3501 76 79 84 97 80 96 5999 5264 .366 2.733 2.917 3.081 2.763 3.197 77 292 2.898 .89 110 4140 5150 53 64 292 303 0 2841 37 2803 1.745 2539 2502 .573 1.862 .803 .897 .803
18 398 2106 115 56 283 2050 296 1842 121 64 181 1786 0 0 327 1332 68 44 66 100 57 100 2333 1967 .138 7.244 9.867 9.626 8.052 3.621 68 280 9.455 .54 100 4280 5140 53 63 307 317 0 1344 36 1309 4.624 1176 1140 .216 6.299 2.209 2.655 2.209
19 1856 2038 114 57 1742 1981 1689 1828 124 66 1575 1771 0 0 1266 1169 56 49 97 100 93 97 3723 3346 .879 1.137 1.124 1.403 1.17 2.725 82 253 1.052 .84 100 4420 5150 54 64 321 331 0 1301 36 1265 .726 1167 1130 1.378 .718 -.462 -.478 -.462
20 1644 2243 119 57 1525 2186 1503 2098 128 71 1384 2041 0 0 1058 1172 58 55 94 100 93 100 3711 3425 .698 1.433 1.475 1.753 1.559 2.982 76 292 1.407 .78 100 4560 5150 54 64 335 345 0 1432 36 1395 .915 1339 1303 1.093 .941 -.128 -.087 -.128

Total number of rows: 41472

Table truncated, full table size 9376 Kbytes.




Supplementary data files not provided
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