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Sample GSM40661 Query DataSets for GSM40661
Status Public on Jan 27, 2006
Title expression array - GBM1
Sample type RNA
 
Channel 1
Source name Cy3: Human Common Reference
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5: GBM1
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: tumor, Brain
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-09/55562
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 = 30.23; Parameter Scan Time = 18:22:25; Parameter PMT Volts = 550; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 6528; 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 = 30.23; Parameter Scan Time = 18:22:25; Parameter PMT Volts = 660; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 180069; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.53; 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
1 331 337 73 55 258 282 280 179 92 77 207 124 0 0 165 487 76 112 93 51 72 36 540 331 .915 1.093 .599 .707 .811 3.7 33 130 5.003 .33 60 1660 5720 77 83 63 69 0 188 31 158 .611 100 69 1.637 .335 -.711 -1.579 -.711
2 6428 1602 73 55 6355 1547 1125 490 83 80 1052 435 0 0 7859 2017 53 166 94 62 92 52 7902 1487 4.108 .243 .413 .237 .245 3.297 101 488 .242 .95 120 1800 5720 74 86 74 86 0 895 31 865 .136 274 243 7.35 .231 -2.878 -2.113 -2.878
3 729 562 72 54 657 508 487 524 82 69 415 470 0 0 774 396 45 74 85 89 75 78 1165 885 1.293 .773 1.133 1.073 .959 4.725 28 131 .525 .72 60 1950 5730 78 84 92 98 0 314 30 284 .432 293 263 2.314 .633 -1.21 -.66 -1.21
4 485 212 72 54 413 158 355 107 76 66 283 53 0 0 349 236 22 51 100 52 92 36 571 336 2.614 .383 .187 .225 .328 6.53 38 173 .319 .46 70 2100 5720 76 83 106 113 0 118 30 88 .214 60 30 4.677 .105 -2.226 -3.256 -2.226
5 293 155 72 55 221 100 203 85 80 76 131 30 0 0 408 176 39 128 70 29 62 10 321 161 2.21 .452 .229 .342 .319 10.48 37 265 .092 .04 80 2230 5720 76 84 119 127 0 87 31 56 .253 48 17 3.954 .128 -1.983 -2.966 -1.983
6 337 358 69 49 268 309 290 160 73 60 221 111 0 0 180 523 15 57 100 62 95 50 577 332 .867 1.153 .502 .603 .717 3.944 24 72 2.897 .6 50 2390 5720 77 82 136 141 0 200 27 173 .644 89 62 1.552 .281 -.634 -1.833 -.634
7 359 628 71 53 288 575 193 461 77 66 122 408 0 0 402 609 33 52 81 89 70 81 863 530 .501 1.997 3.344 2.154 2.422 4.984 37 176 3.628 .32 70 2540 5730 77 84 150 157 0 351 30 321 1.116 258 228 .896 1.869 .158 .902 .158
8 602 924 69 56 533 868 338 719 80 62 269 663 0 0 803 696 52 30 81 100 56 100 1401 932 .614 1.629 2.465 2.881 3.057 1.98 16 80 1.153 .82 50 2680 5720 77 82 165 170 0 516 31 485 .91 402 371 1.099 1.378 -.136 .462 -.136
9 894 1599 73 56 821 1543 671 1687 79 69 598 1631 0 0 685 962 39 54 93 98 92 98 2364 2229 .532 1.879 2.727 2.212 1.727 2.873 66 252 2.031 .7 90 2820 5720 75 84 177 186 0 894 31 862 1.05 943 912 .952 1.524 .071 .608 .071
10 397 265 71 57 326 208 318 180 77 84 247 123 0 0 347 253 43 125 83 50 75 30 534 370 1.567 .638 .498 .392 .585 7.053 72 289 .803 .28 100 2960 5720 75 85 191 201 0 148 32 116 .357 101 69 2.804 .278 -1.488 -1.845 -1.488
11 2778 5622 69 54 2709 5568 2828 6215 93 81 2759 6161 0 0 1934 2994 219 133 86 100 81 100 8277 8920 .487 2.055 2.233 2.641 2.28 2.229 72 271 1.993 .88 100 3120 5720 75 85 207 217 0 3142 30 3112 1.149 3474 3443 .871 1.248 .2 .32 .2
12 6114 30571 71 54 6043 30517 4602 24937 132 72 4531 24883 0 11 5926 27935 835 72 58 100 55 100 36560 29414 .198 5.05 5.492 6.468 5.409 2.566 105 402 4.968 .96 120 3260 5720 74 86 220 232 0 17086 30 17056 2.822 13937 13907 .354 3.069 1.497 1.618 1.497
13 1022 5437 69 57 953 5380 1016 5513 235 88 947 5456 0 0 613 2902 1974 162 7 100 0 98 6333 6403 .177 5.645 5.761 6.93 5.809 2.033 69 222 5.907 .89 90 3410 5710 74 83 236 245 0 3039 32 3007 3.155 3081 3049 .317 3.22 1.658 1.687 1.658
14 203 2328 70 57 133 2271 112 2317 213 89 42 2260 0 0 260 966 1702 158 1 100 0 100 2404 2302 .059 17.075 53.81 46.414 41.286 5.576 79 321 23.027 .31 100 3550 5710 74 84 250 260 0 1301 32 1269 9.543 1295 1263 .105 30.074 3.254 4.91 3.254
15 209 551 70 56 139 495 167 521 76 73 97 465 0 0 174 282 49 69 56 94 49 86 634 562 .281 3.561 4.794 4.411 3.51 5.658 67 200 5.371 .37 90 3700 5710 74 83 265 274 0 308 31 277 1.99 291 260 .502 2.679 .993 1.422 .993
16 27143 20376 71 56 27072 20320 12650 12083 76 71 12579 12027 0 0 26529 19069 33 59 100 99 100 99 47392 24606 1.332 .751 .956 .843 .773 1.954 122 361 .73 .99 120 3850 5720 74 86 279 291 0 11388 31 11357 .42 6753 6722 2.384 .534 -1.253 -.904 -1.253
17 2167 3569 72 58 2095 3511 2117 3686 77 90 2045 3628 0 0 1141 1282 28 132 95 98 95 98 5606 5673 .597 1.676 1.774 1.914 1.873 2.187 67 187 1.64 .83 90 3990 5720 75 84 294 303 0 1995 32 1962 .937 2060 2028 1.068 .992 -.094 -.012 -.094
18 321 2507 70 57 251 2450 229 2239 77 75 159 2182 0 0 241 1387 40 88 77 98 69 98 2701 2341 .102 9.761 13.723 12.558 11.756 2.858 72 226 11.622 .65 90 4140 5710 74 83 309 318 0 1401 32 1369 5.455 1251 1220 .183 7.67 2.448 2.939 2.448
19 2468 2817 68 56 2400 2761 2312 2711 80 88 2244 2655 0 0 1631 1987 63 173 100 97 98 94 5161 4899 .869 1.15 1.183 1.238 1.151 1.958 71 213 1.219 .82 90 4290 5710 74 83 324 333 0 1574 31 1543 .643 1515 1484 1.555 .661 -.637 -.597 -.637
20 1712 2781 69 55 1643 2726 1656 2612 75 109 1587 2557 0 0 1194 1697 41 313 98 97 97 92 4369 4144 .603 1.659 1.611 1.77 1.915 2.181 79 281 1.772 .77 100 4430 5720 75 85 338 348 0 1554 31 1524 .927 1460 1429 1.078 .901 -.109 -.151 -.109

Total number of rows: 41472

Table truncated, full table size 9287 Kbytes.




Supplementary data files not provided
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