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Sample GSM40646 Query DataSets for GSM40646
Status Public on Jan 27, 2006
Title expression array LX-TMZ
Sample type RNA
 
Channel 1
Source name Cy3: Universal Human Reference
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5: LX-TMZ
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: tumor, Brain
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-09/55616.gif
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 = 30.39; Parameter Scan Time = 22:12:22; Parameter PMT Volts = 530; Parameter Scan Date = 2004-08-31; Parameter Pixel Size = 10; Parameter Laser on time = 4660; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.53; 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 = 30.39; Parameter Scan Time = 22:12:22; Parameter PMT Volts = 650; Parameter Scan Date = 2004-08-31; Parameter Pixel Size = 10; Parameter Laser on time = 177944; 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 24, 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 GPL1831
Series (1)
GSE2221 Drug resistance in glioblastoma

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
1 416 867 72 68 344 799 340 425 81 91 268 357 0 0 305 916 34 91 86 95 77 79 1143 625 .431 2.323 1.332 2.286 2.124 2.612 44 136 3.251 .77 70 1630 4670 75 82 67 74 0 464 36 428 1.243 228 191 .804 .713 .314 -.488 .314
2 1402 4042 71 66 1331 3976 1384 3756 93 119 1313 3690 0 0 593 1609 76 156 100 100 100 100 5307 5003 .335 2.987 2.81 3.068 2.932 1.577 152 533 3.193 .89 140 1780 4670 72 86 79 93 0 2164 35 2128 1.599 2011 1975 .625 1.504 .677 .589 .677
3 448 584 71 59 377 525 392 513 91 90 321 454 0 0 257 366 59 94 95 97 88 89 902 775 .718 1.393 1.414 1.496 1.371 2.709 128 457 3.136 .88 130 1920 4670 72 85 93 106 0 313 32 281 .745 275 243 1.341 .757 -.424 -.401 -.424
4 191 145 74 56 117 89 198 131 91 75 124 75 0 0 95 102 50 54 64 56 60 36 206 199 1.315 .761 .605 .775 .692 10.264 25 143 .981 .06 60 2090 4660 75 81 114 120 0 78 30 48 .407 70 40 2.456 .324 -1.296 -1.627 -1.296
5 108 123 74 57 34 66 93 97 84 71 19 40 0 0 49 80 41 45 26 46 21 30 100 59 .515 1.941 2.105 2.264 2.947 5.655 52 191 19.521 .08 80 2220 4700 78 86 126 134 -50 66 31 35 1.039 52 21 .962 1.127 .172 .055
6 204 285 70 57 134 228 154 208 77 79 84 151 0 0 160 261 27 109 85 58 61 30 362 235 .588 1.701 1.798 1.561 1.75 4.711 55 231 2.012 .68 90 2360 4680 75 84 139 148 0 153 31 122 .911 111 81 1.098 .962 -.135 -.055 -.135
7 425 459 70 58 355 401 317 265 75 73 247 207 0 0 403 505 25 56 100 93 87 75 756 454 .885 1.13 .838 1.063 1.3 3.346 33 168 1.239 .88 70 2500 4660 74 81 154 161 0 246 31 215 .605 142 111 1.654 .449 -.726 -1.156 -.726
8 1329 2361 72 62 1257 2299 881 1677 76 87 809 1615 0 0 1300 2054 22 79 98 100 98 100 3556 2424 .547 1.829 1.996 2.063 2.258 2.788 52 306 1.827 .85 110 2640 4690 75 86 166 177 0 1264 33 1231 .979 898 865 1.021 1.069 -.031 .096 -.031
9 872 1568 71 60 801 1508 685 1129 82 103 614 1069 0 0 721 1488 52 129 96 100 93 99 2309 1683 .531 1.883 1.741 1.993 1.762 2.482 117 276 2.142 .87 110 2790 4680 74 85 181 192 0 839 32 807 1.008 604 572 .992 .932 .011 -.102 .011
10 265 516 75 69 190 447 239 431 118 156 164 362 0 0 161 270 101 187 63 86 36 48 637 526 .425 2.353 2.207 3.205 2.296 3.52 52 192 2.757 .49 80 2930 4670 75 83 197 205 -50 276 37 239 1.259 231 194 .794 1.182 .241 .333
11 957 2701 71 58 886 2643 906 2715 91 96 835 2657 0 0 406 688 67 117 99 100 97 100 3529 3492 .335 2.983 3.182 3.306 3.018 1.776 147 549 2.956 .88 140 3090 4670 72 86 210 224 0 1446 31 1415 1.597 1453 1422 .626 1.703 .675 .768 .675
12 3153 6376 71 58 3082 6318 3270 6728 85 74 3199 6670 0 0 1295 1931 60 51 100 100 100 100 9400 9869 .488 2.05 2.085 2.175 2.091 1.444 153 480 1.997 .94 140 3240 4670 72 86 225 239 0 3413 31 3382 1.097 3602 3571 .911 1.116 .134 .159 .134
13 364 896 72 58 292 838 336 889 95 73 264 831 0 0 204 313 85 51 88 100 68 100 1130 1095 .348 2.87 3.148 3.635 3.299 2.696 136 484 2.397 .75 130 3390 4670 72 85 240 253 0 480 31 449 1.536 476 445 .651 1.685 .619 .753 .619
14 179 157 70 69 109 88 161 144 81 104 91 75 0 0 88 73 33 71 71 50 64 28 197 166 1.239 .807 .824 1.704 1.261 6.202 14 69 .36 .05 50 3560 4660 75 80 261 266 0 84 37 47 .432 77 40 2.314 .441 -1.21 -1.181 -1.21
15 146 187 73 60 73 127 93 168 84 82 20 108 0 0 105 91 45 63 46 75 32 42 200 128 .575 1.74 5.4 1.626 .886 6.229 52 217 3.998 .16 80 3670 4660 74 82 271 279 -50 100 32 68 .931 90 58 1.074 2.891 1.531 -.103
16 20221 31898 71 57 20150 31841 20661 33082 81 76 20590 33025 0 0 6152 6605 48 68 100 100 100 100 51991 53615 .633 1.58 1.604 1.642 1.559 1.29 146 422 1.534 .97 130 3820 4660 71 84 283 296 0 17075 31 17045 .846 17709 17679 1.182 .859 -.241 -.22 -.241
17 915 1689 73 57 842 1632 534 1178 94 78 461 1121 0 0 2168 2901 75 73 94 100 92 100 2474 1582 .516 1.938 2.432 2.725 2.353 2.295 138 387 1.699 .98 130 3970 4670 72 85 298 311 0 904 31 874 1.038 631 600 .964 1.302 .053 .38 .053
18 204 117 74 55 130 62 195 93 92 65 121 38 0 0 105 71 58 36 65 51 51 34 192 159 2.097 .477 .314 .438 .318 5.479 52 154 .11 .13 80 4110 4660 74 82 315 323 -50 63 29 33 .255 50 20 3.917 .168 -2.572 -1.97
19 879 1634 73 57 806 1577 843 1646 90 80 770 1589 0 0 351 467 56 74 99 100 97 100 2383 2359 .511 1.957 2.064 2.099 1.954 1.962 141 538 2.04 .84 140 4260 4660 71 85 327 341 0 875 31 844 1.047 881 851 .955 1.105 .067 .144 .067
20 714 1213 71 57 643 1156 633 1208 80 86 562 1151 0 0 324 310 36 95 100 100 100 100 1799 1713 .556 1.798 2.048 1.969 2.077 1.828 133 366 1.829 .76 130 4410 4660 71 84 342 355 0 649 31 619 .962 647 616 1.039 1.096 -.055 .133 -.055

Total number of rows: 41472

Table truncated, full table size 9186 Kbytes.




Supplementary data files not provided
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