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Sample GSM40701 Query DataSets for GSM40701
Status Public on Jan 27, 2006
Title expression array - LGG1
Sample type RNA
 
Channel 1
Source name Cy3: Human Common Reference
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5: LGG1
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: tumor, Brain
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-10/56933
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 = 20:51:02; Parameter PMT Volts = 570; Parameter Scan Date = 2004-10-08; Parameter Pixel Size = 10; Parameter Laser on time = 12099; 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 = 20:51:02; Parameter PMT Volts = 660; Parameter Scan Date = 2004-10-08; Parameter Pixel Size = 10; Parameter Laser on time = 185703; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.54; 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
1 611 746 103 57 508 689 539 569 111 63 436 512 0 0 330 511 39 27 100 97 97 97 1197 948 .737 1.356 1.174 1.131 1.204 2.392 47 221 1.602 .74 80 1680 5090 49 57 48 56 0 410 31 379 .746 313 282 1.34 .646 -.423 -.631 -.423
2 9388 1203 101 56 9287 1147 4081 521 111 71 3980 465 0 0 9368 1242 67 52 100 87 100 77 10434 4445 8.097 .124 .117 .11 .117 2.02 121 426 .121 .94 120 1820 5090 47 59 60 72 0 662 31 631 .068 287 256 14.72 .064 -3.88 -3.96 -3.88
3 1461 1240 97 57 1364 1183 1276 937 123 74 1179 880 0 0 1033 1144 110 52 95 95 93 91 2547 2059 1.153 .867 .746 .679 .722 3.056 45 142 .973 .82 70 1960 5090 49 56 76 83 0 682 31 651 .477 515 484 2.096 .411 -1.068 -1.284 -1.068
4 890 281 97 53 793 228 729 209 106 62 632 156 0 0 614 226 44 33 92 80 90 70 1021 788 3.478 .288 .247 .258 .299 4.531 55 264 .236 .66 90 2120 5090 48 57 91 100 0 155 29 125 .158 115 86 6.323 .136 -2.661 -2.881 -2.661
5 535 178 92 53 443 125 376 123 101 65 284 70 0 0 411 164 38 52 100 55 95 40 568 354 3.544 .282 .246 .198 .321 4.872 47 220 .2 .5 80 2260 5090 49 57 106 114 0 98 29 69 .155 68 39 6.443 .136 -2.688 -2.883 -2.688
6 483 965 98 58 385 907 458 710 108 81 360 652 0 0 297 871 52 81 85 84 80 75 1292 1012 .424 2.356 1.811 2.068 2.104 3.465 57 205 2.969 .84 80 2400 5090 49 57 120 128 0 531 32 499 1.296 391 359 .772 .996 .374 -.005 .374
7 560 493 98 58 462 435 487 444 106 67 389 386 0 0 333 317 48 52 97 89 93 84 897 775 1.062 .942 .992 .905 .78 3.142 46 207 .922 .7 80 2550 5100 50 58 135 143 0 271 32 239 .518 244 212 1.931 .546 -.949 -.873 -.949
8 443 1102 99 55 344 1047 284 627 106 64 185 572 0 0 447 1062 43 40 70 98 61 96 1391 757 .329 3.044 3.092 4.073 4.032 3.728 57 226 3.48 .69 90 2690 5090 48 57 148 157 0 606 30 576 1.674 345 315 .597 1.701 .743 .766 .743
9 1516 1882 99 57 1417 1825 1411 1943 114 72 1312 1886 0 0 842 899 53 51 98 98 98 98 3242 3198 .776 1.288 1.438 1.434 1.374 2.245 92 266 1.249 .87 100 2840 5080 47 57 163 173 0 1035 31 1004 .708 1069 1037 1.412 .791 -.497 -.339 -.497
10 575 457 101 59 474 398 569 390 123 94 468 331 0 0 292 308 91 170 92 78 81 48 872 799 1.191 .84 .707 .81 .635 3.65 88 259 .816 .46 110 2980 5090 47 58 176 187 0 251 32 219 .462 215 182 2.165 .389 -1.114 -1.362 -1.114
11 4231 5806 101 60 4130 5746 4474 5725 116 102 4373 5665 0 0 2231 2960 76 130 98 100 98 100 9876 10038 .719 1.391 1.295 1.443 1.437 1.87 96 295 1.405 .91 110 3130 5080 46 57 191 202 0 3194 33 3161 .765 3149 3116 1.307 .713 -.386 -.489 -.386
12 11348 32895 98 64 11250 32831 12781 39033 110 92 12683 38969 0 0 7102 19757 63 90 100 100 100 100 44081 51652 .343 2.918 3.073 3.13 2.882 1.764 106 296 2.936 .97 110 3280 5080 46 57 206 217 0 18094 35 18059 1.605 21471 21435 .623 1.69 .683 .757 .683
13 1425 3009 97 59 1328 2950 1480 3206 110 73 1383 3147 0 0 574 1266 56 46 100 100 100 100 4278 4530 .45 2.221 2.275 2.261 2.171 1.966 83 301 2.471 .85 110 3420 5080 46 57 220 231 0 1655 32 1623 1.222 1764 1731 .818 1.252 .289 .324 .289
14 304 4715 97 58 207 4657 272 5058 115 81 175 5000 0 0 188 1648 82 117 67 100 51 100 4864 5175 .044 22.498 28.571 32.517 25.75 3.333 109 295 24.556 .65 110 3560 5080 46 57 234 245 0 2594 32 2562 12.375 2782 2750 .081 15.716 3.629 3.974 3.629
15 409 1723 97 58 312 1665 340 1660 113 74 243 1602 0 0 324 625 75 94 77 100 60 100 1977 1845 .187 5.337 6.593 8.457 5.855 3.701 84 239 5.001 .68 100 3710 5080 47 57 250 260 0 948 32 916 2.935 913 881 .341 3.626 1.554 1.859 1.554
16 39656 28879 98 60 39558 28819 45553 33643 114 80 45455 33583 30 0 25670 19053 79 129 100 100 100 100 68377 79038 1.373 .729 .739 .706 .716 1.596 119 393 .728 .98 130 3860 5090 46 59 263 276 0 15885 33 15852 .401 18506 18473 2.495 .406 -1.319 -1.299 -1.319
17 2820 5235 100 57 2720 5178 3006 5657 109 78 2906 5600 0 0 1288 2165 74 162 97 100 97 100 7898 8506 .525 1.904 1.927 2.057 1.851 2.534 88 236 1.949 .9 100 4010 5080 47 57 280 290 0 2880 31 2848 1.047 3112 3080 .955 1.06 .066 .084 .066
18 492 4421 98 57 394 4364 444 4159 102 63 346 4102 0 0 307 1737 37 29 92 100 89 100 4758 4448 .09 11.076 11.855 15.171 11.91 2.611 88 234 11.571 .74 100 4150 5080 47 57 294 304 0 2432 31 2400 6.093 2288 2256 .164 6.521 2.607 2.705 2.607
19 3051 3844 95 55 2956 3789 3079 4128 102 74 2984 4073 0 0 1133 1642 31 96 100 100 100 100 6745 7057 .78 1.282 1.365 1.229 1.342 1.748 92 262 1.346 .9 110 4290 5080 46 57 307 318 0 2114 30 2084 .705 2271 2240 1.418 .751 -.504 -.413 -.504
20 2220 3386 97 55 2123 3331 2122 3620 107 71 2025 3565 0 0 1139 1562 42 55 98 98 97 98 5454 5590 .637 1.569 1.76 1.693 1.553 2.559 98 293 1.594 .89 110 4430 5080 46 57 321 332 0 1863 30 1832 .863 1991 1961 1.159 .968 -.212 -.046 -.212

Total number of rows: 41472

Table truncated, full table size 9437 Kbytes.




Supplementary data files not provided
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