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Sample GSM40675 Query DataSets for GSM40675
Status Public on Jan 27, 2006
Title expression array - BRAIN 3
Sample type RNA
 
Channel 1
Source name Cy3: Human Common Reference
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5: BRAIN 3
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: tumor, Brain
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-10/56921
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 = 31.36; Parameter Scan Time = 19:21:52; Parameter PMT Volts = 560; Parameter Scan Date = 2004-10-08; Parameter Pixel Size = 10; Parameter Laser on time = 12009; 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 = 31.36; Parameter Scan Time = 19:21:52; Parameter PMT Volts = 670; Parameter Scan Date = 2004-10-08; Parameter Pixel Size = 10; Parameter Laser on time = 185614; 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
1 367 124 126 55 241 69 331 110 135 56 205 55 0 0 119 59 46 17 100 87 100 69 310 260 3.493 .286 .268 .254 .263 2.587 33 129 .208 .41 60 1840 5940 79 85 61 67 0 98 44 55 .227 87 44 4.403 .213 -2.139 -2.232 -2.139
2 7976 1475 127 57 7849 1418 3099 518 133 63 2972 461 0 0 8760 1723 47 32 100 90 100 84 9267 3433 5.535 .181 .155 .138 .154 2.372 114 527 .183 .95 130 1980 5940 75 88 71 84 0 1170 45 1125 .143 411 366 6.978 .123 -2.803 -3.023 -2.803
3 940 393 127 57 813 336 866 343 128 64 739 286 0 0 547 282 34 27 100 88 97 88 1149 1025 2.42 .413 .387 .429 .353 2.99 35 139 .344 .66 70 2120 5950 79 86 88 95 0 312 45 267 .328 272 227 3.05 .307 -1.609 -1.704 -1.609
4 712 159 125 56 587 103 562 123 129 58 437 67 0 0 424 114 28 17 100 72 97 61 690 504 5.699 .175 .153 .161 .165 4.193 47 260 .127 .53 80 2280 5940 78 86 104 112 0 126 44 82 .139 98 53 7.185 .122 -2.845 -3.04 -2.845
5 425 96 125 55 300 41 387 74 129 61 262 19 0 0 191 82 34 25 100 41 100 22 341 281 7.317 .137 .073 .112 .124 4.018 36 171 .078 .2 70 2430 5950 79 86 119 126 0 76 44 33 .108 59 15 9.224 .058 -3.205 -4.12 -3.205
6 528 554 126 56 402 498 496 422 134 97 370 366 0 0 230 382 57 202 97 76 91 47 900 736 .807 1.239 .989 1.137 1.095 2.085 34 191 1.577 .78 70 2570 5940 78 85 133 140 0 439 44 395 .983 335 290 1.018 .785 -.025 -.35 -.025
7 421 381 122 59 299 322 354 348 132 92 232 289 0 0 183 230 60 181 100 75 91 27 621 521 .929 1.077 1.246 .899 .799 2.847 37 190 1.555 .53 70 2720 5940 78 85 148 155 0 302 47 255 .854 276 229 1.171 .988 -.227 -.017 -.227
8 453 289 130 57 323 232 441 272 159 63 311 215 0 0 122 167 101 24 100 88 80 84 555 526 1.392 .718 .691 .53 .691 2.402 25 65 .915 .81 50 2870 5930 78 83 164 169 0 229 45 184 .57 216 171 1.755 .548 -.812 -.867 -.812
9 1050 862 124 56 926 806 988 735 134 60 864 679 0 0 553 518 55 27 98 98 98 98 1732 1543 1.149 .87 .786 .938 .894 2.723 74 298 .84 .66 100 3000 5940 77 87 175 185 0 684 44 639 .69 583 539 1.448 .623 -.534 -.682 -.534
10 486 291 130 57 356 234 432 229 137 65 302 172 0 0 248 225 42 64 91 71 86 59 590 474 1.521 .657 .57 .659 .591 4.502 82 322 .589 .49 110 3140 5930 75 86 188 199 0 231 45 186 .521 182 136 1.918 .452 -.94 -1.146 -.94
11 3203 2937 126 59 3077 2878 3268 2689 129 74 3142 2630 0 0 1538 1552 31 83 100 100 100 100 5955 5772 1.069 .935 .837 .928 .962 1.929 85 272 .944 .89 100 3290 5940 77 87 204 214 0 2330 47 2283 .742 2133 2086 1.348 .664 -.431 -.591 -.431
12 9488 12196 121 58 9367 12138 11112 11377 125 70 10991 11319 0 0 5994 8202 36 55 100 100 100 100 21505 22310 .772 1.296 1.03 1.476 1.331 2.019 88 288 1.362 .9 100 3440 5940 77 87 219 229 0 9674 46 9628 1.028 9025 8979 .973 .817 .04 -.292 .04
13 1306 2617 121 57 1185 2560 1190 2439 131 71 1069 2382 0 0 819 1613 85 64 98 100 88 100 3745 3451 .463 2.16 2.228 2.435 2.139 2.231 79 198 2.319 .84 90 3580 5930 76 85 233 242 0 2076 45 2031 1.714 1935 1889 .584 1.768 .777 .822 .777
14 272 1501 123 56 149 1445 213 1342 131 68 90 1286 0 0 175 817 68 56 55 100 39 100 1594 1376 .103 9.698 14.289 12.993 9.707 4.371 89 335 14.911 .44 110 3730 5930 75 86 247 258 0 1191 44 1146 7.693 1065 1020 .13 11.334 2.943 3.503 2.943
15 598 361 123 62 475 299 427 323 126 73 304 261 0 0 1092 220 27 53 92 92 89 82 774 565 1.589 .629 .859 .827 .863 3.523 68 248 .096 .3 100 3880 5940 77 87 263 273 0 286 49 237 .499 256 207 2.003 .681 -1.002 -.554 -1.002
16 27017 12435 124 61 26893 12374 17439 9177 154 117 17315 9116 1 0 25821 11114 206 400 99 97 98 91 39267 26431 2.173 .46 .526 .607 .494 2.051 128 417 .433 .97 130 4020 5930 74 87 275 288 0 9864 48 9815 .365 7279 7231 2.74 .418 -1.454 -1.26 -1.454
17 2316 1899 119 56 2197 1843 2034 1679 129 64 1915 1623 0 0 1130 1246 40 39 100 100 100 100 4040 3538 1.192 .839 .848 .803 .809 1.787 65 271 .903 .87 100 4170 5940 77 87 292 302 0 1506 44 1462 .665 1332 1287 1.503 .672 -.588 -.573 -.588
18 456 3717 122 57 334 3660 407 3834 128 69 285 3777 0 0 259 1784 31 62 94 100 88 100 3994 4062 .091 10.958 13.253 12.913 12.854 2.415 77 197 13.163 .69 90 4310 5930 76 85 306 315 0 2948 45 2903 8.692 3041 2996 .115 10.512 3.12 3.394 3.12
19 2535 1968 123 57 2412 1911 2453 1973 128 67 2330 1916 0 0 1531 956 36 53 100 100 98 100 4323 4246 1.262 .792 .822 .896 .805 2.385 81 258 .7 .88 100 4450 5930 76 86 320 330 0 1561 45 1516 .628 1565 1520 1.591 .652 -.67 -.616 -.67
20 1730 1810 123 59 1607 1751 1742 1817 126 65 1619 1758 0 0 802 823 33 28 100 100 100 100 3358 3377 .918 1.09 1.086 1.098 1.092 2.059 79 272 1.088 .79 100 4590 5940 77 87 334 344 0 1436 47 1389 .864 1441 1394 1.157 .861 -.21 -.215 -.21

Total number of rows: 41472

Table truncated, full table size 9257 Kbytes.




Supplementary data files not provided
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