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Sample GSM40686 Query DataSets for GSM40686
Status Public on Jan 27, 2006
Title expression array - AO2
Sample type RNA
 
Channel 1
Source name Cy3: Human Common Reference
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5: AO2
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: tumor, Brain
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-10/56947
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 = 30.36; Parameter Scan Time = 20:14:39; Parameter PMT Volts = 570; Parameter Scan Date = 2004-10-12; Parameter Pixel Size = 10; Parameter Laser on time = 13098; 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 = 30.36; Parameter Scan Time = 20:14:39; Parameter PMT Volts = 670; Parameter Scan Date = 2004-10-12; Parameter Pixel Size = 10; Parameter Laser on time = 186703; 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) [email protected]
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
1 491 154 145 57 346 97 440 89 158 62 295 32 0 0 392 117 131 28 95 60 64 40 443 327 3.567 .28 .108 .197 .145 3.532 45 261 .156 .46 80 1610 5120 64 72 41 49 0 101 37 64 .184 58 21 5.444 .071 -2.445 -3.815 -2.445
2 10059 7338 147 57 9912 7281 3017 2625 160 70 2870 2568 0 0 11160 8322 100 74 85 90 78 85 17193 5438 1.361 .735 .895 .895 .747 3.467 95 487 .734 .97 120 1760 5120 62 74 54 66 0 4808 37 4770 .481 1720 1682 2.078 .586 -1.055 -.77 -1.055
3 1012 534 146 55 866 479 829 398 157 62 683 343 0 0 556 452 68 30 100 97 100 77 1345 1026 1.808 .553 .502 .368 .391 3.735 36 158 .51 .57 70 1910 5130 65 72 71 78 0 350 36 314 .362 261 225 2.759 .329 -1.464 -1.604 -1.464
4 445 101 143 55 302 46 397 77 159 60 254 22 0 0 246 70 109 26 73 45 59 23 348 276 6.565 .152 .087 .122 .149 5.367 42 324 .09 .35 90 2050 5110 62 71 84 93 0 66 36 30 .1 50 14 10.021 .057 -3.325 -4.139 -3.325
5 415 133 147 58 268 75 321 81 164 64 174 23 0 0 228 126 122 32 81 42 28 26 343 197 3.573 .28 .132 .179 .168 4.199 38 179 .058 .13 70 2200 5120 64 71 100 107 0 87 38 49 .183 53 15 5.454 .087 -2.447 -3.529 -2.447
6 467 92 146 57 321 35 458 71 157 69 312 14 0 0 101 92 62 52 100 14 100 5 356 326 9.171 .109 .045 .05 .052 4.221 35 193 .076 .16 70 2340 5120 64 71 114 121 0 60 37 23 .071 47 9 13.999 .029 -3.807 -5.088 -3.807
7 453 301 144 60 309 241 387 164 147 68 243 104 0 0 202 331 42 41 96 72 87 60 550 347 1.282 .78 .428 .496 .403 3.936 33 191 1.446 .45 70 2490 5120 64 71 129 136 0 197 39 158 .511 107 68 1.957 .28 -.969 -1.834 -.969
8 546 683 143 59 403 624 502 371 148 71 359 312 0 0 210 975 37 47 100 96 96 92 1027 671 .646 1.548 .869 .944 .885 3.022 28 127 5.083 .51 60 2640 5120 65 71 145 151 0 447 39 409 1.014 243 204 .986 .569 .021 -.812 .021
9 803 593 139 58 664 535 677 477 155 68 538 419 0 0 602 412 96 44 87 97 78 91 1199 957 1.241 .806 .779 .938 .72 4.919 73 297 .544 .48 100 2760 5120 63 73 155 165 0 389 38 351 .528 313 275 1.894 .51 -.922 -.971 -.922
10 735 352 136 59 599 293 574 247 145 74 438 188 0 0 529 351 58 62 93 74 86 63 892 626 2.044 .489 .429 .368 .394 6.353 74 276 .415 .55 100 2910 5120 63 73 170 180 0 231 39 192 .32 162 123 3.12 .281 -1.642 -1.83 -1.642
11 3283 9129 137 60 3146 9069 2949 8926 144 73 2812 8866 0 0 1469 3436 58 56 100 100 98 100 12215 11678 .347 2.883 3.153 3.049 3.081 1.71 81 295 3.035 .89 100 3060 5120 63 73 185 195 0 5981 39 5942 1.889 5848 5809 .529 2.066 .917 1.047 .917
12 13069 30055 134 57 12935 29998 15902 36324 146 63 15768 36267 0 0 7282 15572 69 34 97 100 96 100 42933 52035 .431 2.319 2.3 2.919 2.306 2.28 82 310 2.316 .97 100 3210 5120 63 73 200 210 0 19691 37 19654 1.519 23798 23761 .658 1.507 .604 .592 .604
13 1816 2833 131 58 1685 2775 1682 2744 141 64 1551 2686 0 0 894 1223 59 42 100 100 95 98 4460 4237 .607 1.647 1.732 1.753 1.565 2.744 65 231 1.8 .75 90 3350 5120 63 72 214 223 0 1856 38 1818 1.079 1798 1760 .927 1.135 .11 .182 .11
14 231 1056 132 60 99 996 178 862 142 69 46 802 0 0 130 755 64 46 36 100 28 97 1095 848 .099 10.061 17.435 13.769 16.191 4.206 94 327 18.802 .34 110 3500 5120 62 73 228 239 0 692 39 653 6.591 565 525 .152 11.423 2.721 3.514 2.721
15 227 7515 137 59 90 7456 160 7537 152 70 23 7478 0 0 178 2921 73 55 28 100 19 100 7546 7501 .012 82.844 325.13 128.432 154.467 4.016 91 262 94.418 .35 100 3650 5120 63 73 244 254 0 4924 39 4885 54.277 4938 4899 .018 213.016 5.762 7.735 5.762
16 37870 35969 131 57 37739 35912 43438 40999 141 78 43307 40942 3 2 22624 20628 64 154 100 100 100 100 73651 84249 1.051 .952 .945 1.091 .967 1.668 93 302 .937 .98 110 3800 5120 62 73 258 269 0 23566 37 23528 .623 26861 26824 1.604 .619 -.682 -.691 -.682
17 2608 5717 130 58 2478 5659 2639 5600 140 89 2509 5542 0 0 1404 2313 62 189 100 100 98 100 8137 8051 .438 2.284 2.209 2.608 2.398 2.018 65 197 2.337 .85 90 3940 5120 63 72 273 282 0 3746 38 3708 1.496 3669 3631 .668 1.447 .581 .533 .581
18 583 4379 127 59 456 4320 429 4509 139 70 302 4450 0 0 449 1781 71 54 90 100 74 100 4776 4752 .106 9.474 14.735 13.398 11.371 3.119 75 292 12.673 .52 100 4080 5110 62 72 287 297 0 2869 39 2830 6.207 2954 2916 .161 9.654 2.634 3.271 2.634
19 2308 2780 130 60 2178 2720 2176 2574 147 82 2046 2514 0 0 1131 1448 115 92 100 100 100 100 4898 4560 .801 1.249 1.229 1.256 1.287 1.956 77 267 1.315 .83 100 4240 5120 63 73 303 313 0 1821 39 1782 .818 1686 1647 1.222 .805 -.289 -.313 -.289
20 2175 3915 128 61 2047 3854 2069 3772 139 72 1941 3711 0 0 978 2078 100 54 100 100 98 100 5901 5652 .531 1.883 1.912 1.89 1.857 1.722 79 281 2.151 .85 100 4380 5120 63 73 317 327 0 2565 40 2525 1.234 2471 2431 .811 1.253 .303 .325 .303

Total number of rows: 41472

Table truncated, full table size 9218 Kbytes.




Supplementary data files not provided
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