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Sample GSM40707 Query DataSets for GSM40707
Status Public on Jan 27, 2006
Title expression array - GBM30
Sample type RNA
 
Channel 1
Source name Cy3: Human Common Reference
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5: GBM30
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: tumor, Brain
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-10/56952
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 = 31.48; Parameter Scan Time = 22:54:56; Parameter PMT Volts = 560; Parameter Scan Date = 2004-10-12; Parameter Pixel Size = 10; Parameter Laser on time = 13258; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.43; 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 = 31.48; Parameter Scan Time = 22:54:56; Parameter PMT Volts = 670; Parameter Scan Date = 2004-10-12; Parameter Pixel Size = 10; Parameter Laser on time = 186863; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.58; 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
1 367 83 109 54 258 29 383 66 116 76 274 12 0 0 86 52 40 124 100 4 100 0 287 286 8.897 .112 .044 .106 .076 3.27 44 168 .062 .16 70 1770 5210 61 68 57 64 0 69 45 24 .094 55 10 10.681 .036 -3.417 -4.777 -3.417
2 8033 2452 104 54 7929 2398 4601 1040 115 62 4497 986 0 0 8313 2644 48 47 98 82 95 77 10327 5483 3.307 .302 .219 .29 .295 2.663 93 382 .302 .96 110 1910 5220 60 71 69 80 0 2042 45 1997 .252 866 821 3.97 .183 -1.989 -2.453 -1.989
3 565 228 103 54 462 174 519 187 113 58 416 133 0 0 263 201 43 18 100 72 100 62 636 549 2.655 .377 .32 .187 .256 4.397 37 178 .456 .76 70 2060 5220 62 69 86 93 0 190 45 145 .314 156 111 3.188 .266 -1.672 -1.909 -1.672
4 407 134 104 56 303 78 407 83 107 61 303 27 0 0 167 156 26 26 97 50 94 33 381 330 3.885 .257 .089 .148 .157 4.787 36 281 .068 .08 80 2230 5220 62 70 103 111 0 112 47 65 .214 69 22 4.664 .074 -2.221 -3.752 -2.221
5 308 81 105 57 203 24 257 65 119 68 152 8 0 0 125 50 87 52 90 14 42 9 227 160 8.458 .118 .053 .1 .098 5.284 42 148 .035 .1 70 2360 5220 62 69 116 123 0 67 47 20 .098 54 7 10.155 .044 -3.344 -4.512 -3.344
6 341 270 110 57 231 213 357 100 127 67 247 43 0 0 147 314 77 42 80 50 65 44 444 290 1.085 .922 .174 .441 .48 10.555 52 261 2.363 .29 90 2490 5230 62 71 128 137 0 225 47 177 .768 83 36 1.302 .145 -.381 -2.786 -.381
7 384 112 116 54 268 58 359 71 130 63 243 17 0 0 100 100 64 30 100 41 93 25 326 260 4.621 .216 .07 .14 .118 3.445 31 58 .291 .45 50 2650 5210 62 67 146 151 0 93 45 48 .18 59 14 5.547 .058 -2.472 -4.101 -2.472
8 471 133 116 54 355 79 434 84 127 81 318 30 0 0 167 95 50 107 100 28 96 7 434 348 4.494 .223 .094 .117 .119 5.52 28 143 .147 .33 60 2800 5220 63 69 161 167 0 111 45 66 .185 70 25 5.395 .079 -2.432 -3.67 -2.432
9 627 456 111 53 516 403 557 361 115 58 446 308 0 0 377 385 32 23 100 98 96 96 919 754 1.28 .781 .691 .721 .73 3.479 64 203 .765 .43 90 2930 5230 62 71 172 181 0 380 44 336 .651 301 257 1.537 .575 -.62 -.798 -.62
10 692 140 113 55 579 85 540 111 119 65 427 56 0 0 398 92 33 68 98 43 98 20 664 483 6.812 .147 .131 .114 .159 5.096 74 252 .057 .21 100 3080 5220 61 71 187 197 0 117 46 71 .122 92 47 8.178 .109 -3.032 -3.194 -3.032
11 2359 1656 120 56 2239 1600 2335 1578 130 59 2215 1522 0 0 998 687 48 20 100 100 100 100 3839 3737 1.399 .715 .687 .727 .739 1.819 84 265 .668 .86 100 3220 5220 61 71 201 211 0 1379 47 1333 .595 1314 1268 1.68 .572 -.748 -.805 -.748
12 10096 34269 117 56 9979 34213 12325 41645 126 66 12208 41589 0 0 6454 20462 46 43 98 100 98 100 44192 53797 .292 3.428 3.407 3.943 3.567 1.688 99 296 3.378 .98 110 3370 5220 60 71 215 226 0 28545 47 28498 2.856 34688 34642 .35 2.838 1.514 1.505 1.514
13 1322 7641 117 54 1205 7587 1261 7938 121 63 1144 7884 0 0 731 3060 32 36 100 100 100 100 8792 9028 .159 6.296 6.892 7.084 6.844 1.854 84 257 6.585 .85 100 3520 5220 61 71 231 241 0 6365 45 6320 5.244 6612 6567 .191 5.74 2.391 2.521 2.391
14 230 252 120 56 110 196 166 214 124 69 46 158 0 0 128 162 33 50 56 83 47 63 306 204 .561 1.782 3.435 1.825 1.54 5.712 55 305 3.259 .24 100 3660 5210 60 70 245 255 0 210 47 163 1.484 178 132 .674 2.861 .57 1.517 .57
15 339 49007 123 59 216 48948 281 55908 127 67 158 55849 0 2 191 16189 33 35 88 100 80 100 49164 56007 .004 226.611 353.475 290.568 277.995 2.23 104 318 231.619 .71 110 3810 5210 59 70 259 270 0 40821 49 40771 188.757 46569 46520 .005 294.428 7.56 8.202 7.56
16 37426 30428 124 61 37302 30367 40199 33443 150 87 40075 33382 0 0 16496 12055 163 89 100 100 100 100 67669 73457 1.228 .814 .833 .846 .813 1.203 87 259 .793 .99 100 3950 5220 61 71 274 284 0 25345 51 25294 .678 27856 27806 1.475 .694 -.56 -.527 -.56
17 1862 4461 124 59 1738 4402 1722 4453 151 91 1598 4394 0 0 1023 1469 170 101 100 100 98 100 6140 5992 .395 2.533 2.75 2.805 2.766 1.737 73 209 2.515 .82 90 4100 5210 60 69 289 298 0 3716 49 3667 2.11 3709 3660 .474 2.29 1.077 1.196 1.077
18 532 1269 121 55 411 1214 436 1150 126 62 315 1095 0 0 451 600 40 33 88 98 85 98 1625 1410 .339 2.954 3.476 3.851 3.398 3.631 81 233 3.524 .48 100 4250 5220 61 71 304 314 0 1057 46 1011 2.46 958 912 .406 2.896 1.299 1.534 1.299
19 1876 1246 118 54 1758 1192 1759 1044 124 62 1641 990 0 0 948 947 37 38 100 100 100 100 2950 2631 1.475 .678 .603 .635 .538 2.185 89 225 .742 .77 100 4390 5220 61 71 318 328 0 1038 45 993 .565 870 825 1.771 .503 -.824 -.993 -.824
20 1981 2037 116 55 1865 1982 1935 2019 126 60 1819 1964 0 0 984 870 50 27 100 100 97 100 3847 3783 .941 1.063 1.08 1.18 1.025 2.091 84 271 1.012 .88 100 4530 5220 61 71 332 342 0 1697 46 1651 .885 1682 1636 1.13 .899 -.176 -.153 -.176

Total number of rows: 41472

Table truncated, full table size 9074 Kbytes.




Supplementary data files not provided
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