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Sample GSM40669 Query DataSets for GSM40669
Status Public on Jan 27, 2006
Title expression array - GBM31
Sample type RNA
 
Channel 1
Source name Cy3: Human Common Reference
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5: GBM31
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: tumor, Brain
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-09/55566
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 = 31.82; Parameter Scan Time = 20:24:39; Parameter PMT Volts = 550; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 6648; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.48; 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 = 31.82; Parameter Scan Time = 20:24:39; Parameter PMT Volts = 660; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 180189; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.56; 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
1 501 754 86 57 415 697 427 388 97 73 341 331 0 0 232 1148 49 66 100 83 100 77 1112 672 .595 1.68 .971 .873 1.325 4.65 31 123 8.924 .31 60 1730 4920 69 75 58 64 0 340 26 314 .757 175 149 1.321 .437 -.402 -1.193 -.402
2 4427 20178 84 55 4343 20123 557 3239 95 85 473 3184 0 18 6474 26254 53 144 89 100 83 100 24466 3657 .216 4.633 6.732 7.858 5.309 3.558 128 536 4.343 .96 130 1870 4920 65 78 68 81 0 9092 25 9068 2.088 1460 1435 .479 3.033 1.062 1.601 1.062
3 933 932 85 61 848 871 890 699 94 123 805 638 0 0 712 931 49 227 87 87 80 64 1719 1443 .974 1.027 .793 1.235 .954 2.606 31 134 1.21 .88 60 2020 4920 69 75 87 93 0 420 27 392 .463 315 287 2.161 .357 -1.111 -1.485 -1.111
4 668 462 83 61 585 401 527 321 99 102 444 260 0 0 658 414 56 236 92 52 76 26 986 704 1.459 .685 .586 .665 .507 4.256 38 138 .448 .49 60 2170 4920 69 75 102 108 0 208 27 181 .309 145 117 3.238 .264 -1.695 -1.922 -1.695
5 366 272 84 57 282 215 324 226 104 72 240 169 0 0 197 242 162 57 63 69 39 60 497 409 1.312 .762 .704 .579 .625 5.119 33 194 .988 .34 70 2310 4920 68 75 115 122 0 123 26 97 .344 102 76 2.911 .317 -1.541 -1.656 -1.541
6 396 471 85 53 311 418 376 374 92 63 291 321 0 0 208 389 40 41 93 90 83 77 729 612 .744 1.344 1.103 1.136 1.189 3.024 31 178 1.746 .77 70 2460 4920 68 75 130 137 0 212 24 188 .606 169 145 1.651 .497 -.723 -1.009 -.723
7 300 331 83 55 217 276 204 247 92 62 121 192 0 0 296 282 39 42 75 73 55 73 493 313 .786 1.272 1.587 1.404 1.334 6.985 45 244 1.127 .53 80 2600 4920 68 76 144 152 0 149 25 124 .573 111 87 1.745 .715 -.803 -.484 -.803
8 414 592 81 51 333 541 279 463 88 66 198 412 0 0 372 397 34 58 87 95 58 95 874 610 .616 1.625 2.081 2.582 3.489 3.681 24 134 1.614 .59 60 2760 4920 69 75 161 167 0 267 23 244 .732 209 186 1.366 .938 -.45 -.093 -.45
9 1053 1424 81 56 972 1368 754 1205 91 89 673 1149 0 0 834 852 45 168 90 95 88 93 2340 1822 .711 1.407 1.707 2.057 1.54 4.338 60 214 1.28 .82 90 2900 4920 67 76 173 182 0 642 25 616 .634 543 518 1.577 .769 -.657 -.378 -.657
10 587 401 84 54 503 347 492 301 101 72 408 247 0 0 387 402 81 129 94 65 91 47 850 655 1.45 .69 .605 .429 .49 5.737 67 270 .703 .44 100 3040 4920 67 77 187 197 0 181 24 156 .311 136 111 3.217 .273 -1.686 -1.874 -1.686
11 3108 5523 85 57 3023 5466 3271 5793 97 77 3186 5736 0 0 2124 3293 68 77 97 100 94 98 8489 8922 .553 1.808 1.8 2.284 1.966 3.168 71 274 1.827 .88 100 3190 4920 67 77 202 212 0 2489 26 2463 .815 2610 2585 1.227 .811 -.296 -.302 -.296
12 6632 22364 83 55 6549 22309 3424 17163 92 81 3341 17108 0 0 6887 21358 45 119 85 100 81 99 28858 20449 .294 3.406 5.121 5.4 3.86 3.373 100 452 3.381 .95 120 3330 4910 65 77 215 227 0 10077 25 10053 1.535 7734 7709 .651 2.307 .618 1.206 .618
13 1502 4790 83 54 1419 4736 1395 5242 102 75 1312 5188 0 0 1005 1952 78 90 96 100 93 98 6155 6500 .3 3.338 3.954 3.706 3.737 2.573 62 235 3.542 .77 90 3480 4910 66 75 231 240 0 2158 24 2134 1.504 2362 2338 .665 1.782 .589 .833 .589
14 178 2945 82 56 96 2889 113 2912 96 73 31 2856 0 0 177 1370 68 72 31 100 24 100 2985 2887 .033 30.094 92.129 51.186 39.083 4.319 77 330 28.532 .46 100 3620 4910 66 76 245 255 0 1327 25 1302 13.56 1312 1287 .074 41.514 3.761 5.376 3.761
15 379 3621 85 55 294 3566 237 3758 96 62 152 3703 0 0 474 1743 47 36 69 100 59 100 3860 3855 .082 12.129 24.362 25.84 18.161 4.872 66 204 11.681 .54 90 3770 4910 66 75 260 269 0 1632 25 1607 5.466 1693 1669 .183 10.978 2.45 3.456 2.45
16 24158 22826 84 56 24074 22770 3170 4299 96 72 3086 4243 1 0 27615 25329 75 67 99 99 99 96 46844 7329 1.057 .946 1.375 .96 .932 2.35 128 437 .924 .96 130 3910 4920 65 78 272 285 0 10286 25 10260 .426 1937 1912 2.346 .62 -1.23 -.691 -1.23
17 2276 5590 83 57 2193 5533 2076 5975 88 72 1993 5918 0 0 1352 2784 34 80 98 100 96 98 7726 7911 .396 2.523 2.969 2.708 2.815 2.765 64 204 2.627 .86 90 4070 4910 66 75 290 299 0 2519 26 2493 1.137 2692 2667 .88 1.338 .185 .42 .185
18 486 3947 82 57 404 3890 337 3989 88 77 255 3932 0 0 485 2021 32 75 80 100 73 100 4294 4187 .104 9.629 15.42 17.062 14.268 3.684 68 214 10.388 .6 90 4210 4910 66 75 304 313 0 1779 26 1753 4.339 1797 1772 .23 6.948 2.117 2.797 2.117
19 2333 5504 81 58 2252 5446 2170 5915 90 81 2089 5857 0 0 1439 3070 55 93 97 100 97 100 7698 7946 .414 2.418 2.804 2.772 2.519 2.687 67 293 2.536 .88 100 4360 4910 66 76 319 329 0 2480 26 2454 1.09 2665 2639 .918 1.263 .124 .337 .124
20 2209 4422 81 55 2128 4367 2265 4308 89 73 2184 4253 0 0 1092 2290 47 78 97 100 95 100 6495 6437 .487 2.052 1.947 2.229 2.003 2.528 70 303 2.311 .84 100 4500 4910 66 76 333 343 0 1993 25 1968 .925 1941 1916 1.081 .877 -.113 -.189 -.113

Total number of rows: 41472

Table truncated, full table size 9323 Kbytes.




Supplementary data files not provided

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