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Sample GSM40672 Query DataSets for GSM40672
Status Public on Jan 27, 2006
Title expression array - GBM27
Sample type RNA
 
Channel 1
Source name Cy3: Human Common Reference
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5: GBM27
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: tumor, Brain
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-10/56904
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 = 30.48; Parameter Scan Time = 18:09:59; Parameter PMT Volts = 550; Parameter Scan Date = 2004-10-05; Parameter Pixel Size = 10; Parameter Laser on time = 10977; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.45; 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 = 30.48; Parameter Scan Time = 18:09:59; Parameter PMT Volts = 660; Parameter Scan Date = 2004-10-05; Parameter Pixel Size = 10; Parameter Laser on time = 184582; 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) [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
1 366 732 79 56 287 676 338 550 86 77 259 494 0 0 181 506 27 96 96 96 93 90 963 753 .425 2.355 1.907 2.289 2.491 2.491 32 115 3.442 .71 60 1710 5590 64 70 48 54 0 493 38 456 1.587 371 333 .63 1.285 .667 .362 .667
2 5082 11360 78 57 5004 11303 813 2159 90 67 735 2102 0 0 6595 14342 72 42 90 99 84 97 16307 2837 .443 2.259 2.86 2.477 2.376 2.577 110 358 2.226 .98 110 1850 5600 62 73 59 70 0 7656 38 7617 1.522 1455 1417 .657 1.927 .606 .947 .606
3 676 368 79 59 597 309 710 364 88 65 631 305 0 0 333 221 33 30 96 90 96 87 906 936 1.932 .518 .483 .485 .428 2.586 32 144 .482 .73 60 2000 5600 65 71 77 83 0 248 40 208 .349 245 206 2.867 .326 -1.52 -1.618 -1.52
4 335 191 80 58 255 133 298 89 106 77 218 31 0 0 141 220 82 64 92 45 75 30 388 249 1.917 .522 .142 .297 .465 7.89 40 229 .947 .28 80 2150 5600 64 72 91 99 0 129 39 90 .351 60 21 2.845 .096 -1.508 -3.383 -1.508
5 236 99 78 57 158 42 188 72 79 70 110 15 0 0 127 79 22 54 97 25 97 13 200 125 3.762 .266 .136 .227 .168 5.272 36 170 .168 .22 70 2280 5600 64 71 104 111 0 67 38 28 .179 49 10 5.582 .092 -2.481 -3.444 -2.481
6 250 89 79 57 171 32 210 65 81 67 131 8 0 0 114 88 21 37 100 17 97 8 203 139 5.344 .187 .061 .141 .124 3.538 35 178 .236 .3 70 2430 5600 64 71 119 126 0 60 38 22 .126 44 5 7.93 .041 -2.987 -4.603 -2.987
7 206 180 77 57 129 123 177 137 85 75 100 80 0 0 121 229 37 66 72 59 59 27 252 180 1.049 .953 .8 .995 .835 5.277 47 261 3.87 .26 80 2580 5600 64 72 134 142 0 121 38 83 .643 92 54 1.556 .539 -.638 -.891 -.638
8 240 249 80 63 160 186 207 192 97 92 127 129 0 0 110 183 56 88 84 52 63 47 346 256 .86 1.163 1.016 .981 1.357 4.364 19 71 1.749 .71 50 2720 5620 67 72 149 154 0 168 42 125 .783 129 87 1.276 .685 -.352 -.547 -.352
9 734 500 78 54 656 446 695 521 86 61 617 467 0 0 374 256 36 31 98 98 98 96 1102 1084 1.471 .68 .757 .673 .727 2.411 56 213 .59 .72 80 2870 5600 64 72 163 171 0 337 36 301 .458 351 315 2.183 .51 -1.126 -.971 -1.126
10 541 192 76 55 465 137 497 133 84 74 421 78 0 0 290 153 40 66 100 56 100 38 602 499 3.394 .295 .185 .18 .22 4.459 62 189 .185 .4 80 3010 5600 64 72 177 185 0 129 37 92 .199 90 53 5.037 .125 -2.332 -3.002 -2.332
11 2591 2983 73 58 2518 2925 2684 3020 77 80 2611 2962 0 0 1173 1612 22 89 100 100 98 100 5443 5573 .861 1.162 1.134 1.114 1.077 1.84 70 240 1.237 .9 90 3160 5590 62 71 191 200 0 2010 39 1971 .783 2035 1996 1.277 .764 -.353 -.387 -.353
12 8360 18981 76 55 8284 18926 7952 19772 80 78 7876 19717 0 0 6257 14311 22 88 100 100 97 100 27210 27593 .438 2.285 2.503 2.597 2.316 1.858 88 333 2.305 .99 110 3300 5600 62 73 204 215 0 12791 37 12754 1.54 13324 13287 .65 1.687 .623 .755 .623
13 1309 3846 74 57 1235 3789 1324 3916 82 71 1250 3859 0 0 783 1842 29 54 100 100 95 100 5024 5109 .326 3.068 3.087 3.475 3.463 2.1 72 233 3.235 .84 90 3450 5590 62 71 220 229 0 2592 38 2553 2.068 2639 2601 .484 2.08 1.048 1.057 1.048
14 193 396 77 58 116 338 170 354 86 81 93 296 0 0 101 172 34 132 71 90 58 63 454 389 .343 2.914 3.183 3.478 2.718 3.816 63 239 4.97 .58 90 3590 5600 63 72 234 243 0 267 39 228 1.964 239 199 .509 2.145 .974 1.101 .974
15 223 12076 78 58 145 12018 155 12388 88 85 77 12330 0 0 192 6603 43 131 64 100 49 98 12163 12407 .012 82.883 160.13 127.544 107.183 4.196 85 275 114.103 .35 100 3750 5600 63 73 250 260 0 8138 39 8099 55.855 8348 8309 .018 107.912 5.804 6.754 5.804
16 24470 17546 77 59 24393 17487 17132 14042 90 78 17055 13983 0 0 23087 16443 61 77 100 100 100 100 41880 31038 1.395 .717 .82 .784 .729 1.635 110 436 .712 .99 130 3890 5600 61 74 262 275 0 11824 40 11785 .483 9463 9423 2.07 .553 -1.05 -.856 -1.05
17 1826 4265 74 60 1752 4205 1807 4217 88 75 1733 4157 0 0 994 2084 57 49 98 100 98 100 5957 5890 .417 2.4 2.399 2.57 2.49 1.684 69 224 2.412 .94 90 4040 5590 62 71 279 288 0 2874 40 2834 1.617 2842 2801 .618 1.617 .694 .693 .694
18 428 2558 75 56 353 2502 326 2674 79 66 251 2618 0 0 327 791 31 41 92 100 88 100 2855 2869 .141 7.088 10.43 9.576 9.569 2.26 68 231 6.826 .73 90 4180 5590 62 71 293 302 0 1724 38 1686 4.777 1802 1764 .209 7.029 2.256 2.813 2.256
19 2138 2254 75 56 2063 2198 2304 2108 89 73 2229 2052 0 0 1011 1034 99 51 100 100 98 100 4261 4281 .939 1.065 .921 1.097 .981 1.771 67 183 1.053 .88 80 4330 5600 64 72 309 317 0 1519 38 1481 .718 1421 1383 1.393 .62 -.478 -.689 -.478
20 1920 2018 75 58 1845 1960 1877 2088 88 75 1802 2030 0 0 1063 1113 91 73 100 100 95 100 3805 3832 .941 1.062 1.127 1.082 1.083 1.747 73 226 1.059 .86 90 4470 5590 62 71 322 331 0 1360 39 1321 .716 1407 1368 1.397 .759 -.482 -.398 -.482

Total number of rows: 41472

Table truncated, full table size 9223 Kbytes.




Supplementary data files not provided
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