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Sample GSM40673 Query DataSets for GSM40673
Status Public on Jan 27, 2006
Title expression array - GBM4
Sample type RNA
 
Channel 1
Source name Cy3: Human Common Reference
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5: GBM4
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: tumor, Brain
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-09/55569
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 = 29.90; Parameter Scan Time = 17:57:56; Parameter PMT Volts = 550; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 6502; 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 = 29.90; Parameter Scan Time = 17:57:56; Parameter PMT Volts = 660; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 180043; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.52; 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
1 259 197 75 53 184 144 247 152 77 59 172 99 0 0 80 143 22 33 100 75 100 63 328 271 1.278 .783 .576 .513 .706 3.597 41 156 1.376 .49 70 1890 5240 68 75 65 72 0 124 33 90 .491 95 62 2.036 .361 -1.026 -1.469 -1.026
2 2236 10570 75 52 2161 10518 413 1154 80 62 338 1102 0 0 3231 15477 41 69 88 98 74 96 12679 1440 .205 4.867 3.26 4.866 4.795 2.793 134 534 4.943 .97 130 2030 5230 64 77 76 89 0 6633 33 6600 3.054 724 692 .327 2.046 1.611 1.033 1.611
3 544 333 76 55 468 278 521 288 79 64 445 233 0 0 417 265 35 41 89 93 72 75 746 678 1.683 .594 .524 .762 .85 3.984 29 121 .499 .59 60 2180 5250 70 76 95 101 0 209 35 174 .373 181 146 2.683 .329 -1.424 -1.606 -1.424
4 416 145 74 53 342 92 348 72 81 62 274 19 0 0 288 132 38 41 100 38 93 36 434 293 3.717 .269 .069 .178 .129 5.218 44 260 .147 .3 80 2330 5240 68 76 109 117 0 91 33 58 .169 45 12 5.924 .044 -2.567 -4.522 -2.567
5 267 158 74 56 193 102 173 99 82 64 99 43 0 0 293 130 43 38 88 52 60 44 295 142 1.892 .528 .434 .597 .581 9.91 25 185 .173 .28 70 2470 5230 67 74 123 130 0 99 35 64 .332 62 27 3.015 .273 -1.592 -1.875 -1.592
6 280 111 71 54 209 57 258 70 77 62 187 16 0 0 125 123 31 33 96 28 93 15 266 203 3.667 .273 .086 .15 .118 5.393 32 155 .102 .06 60 2610 5230 68 74 138 144 0 70 34 36 .171 44 10 5.843 .054 -2.547 -4.219 -2.547
7 309 306 71 55 238 251 205 226 80 59 134 171 0 0 314 257 50 22 89 79 72 75 489 305 .948 1.055 1.276 1.052 1.187 6.491 29 143 .755 .33 60 2750 5240 69 75 152 158 0 192 35 158 .662 142 107 1.511 .801 -.596 -.32 -.596
8 292 362 77 56 215 306 255 222 123 88 178 166 0 0 204 350 385 168 15 50 3 38 521 344 .703 1.423 .933 1.529 1.702 5.207 26 143 3.443 .41 60 2910 5230 68 74 168 174 0 227 35 192 .893 139 104 1.12 .585 -.163 -.773 -.163
9 652 785 74 51 578 734 516 625 85 62 442 574 0 0 474 594 55 53 92 93 90 92 1312 1016 .787 1.27 1.299 1.024 1.191 3.626 64 228 1.558 .51 90 3050 5230 66 75 180 189 0 493 32 461 .797 392 360 1.255 .815 -.328 -.295 -.328
10 293 194 75 55 218 139 215 132 82 64 140 77 0 0 294 184 38 47 72 60 56 44 357 217 1.568 .638 .55 .8 .895 8.742 79 274 .219 .21 110 3200 5240 66 77 194 205 0 122 35 87 .4 83 48 2.499 .345 -1.321 -1.535 -1.321
11 1467 1908 73 55 1394 1853 1396 1742 85 67 1323 1687 0 0 1077 1353 105 83 85 94 83 89 3247 3010 .752 1.329 1.275 1.631 1.421 3.194 85 309 1.381 .8 110 3340 5230 65 76 208 219 0 1197 35 1163 .834 1093 1059 1.199 .8 -.262 -.322 -.262
12 3669 11144 72 55 3597 11089 4120 12099 83 70 4048 12044 0 0 2850 8487 103 90 91 100 83 98 14686 16092 .324 3.083 2.975 3.534 3.03 2.366 90 317 3.182 .94 110 3490 5230 65 76 223 234 0 6993 35 6959 1.935 7593 7558 .517 1.867 .952 .901 .952
13 649 2042 71 55 578 1987 587 2122 78 65 516 2067 0 0 459 1044 56 55 88 98 84 98 2565 2583 .291 3.438 4.006 4.288 3.545 4.457 71 208 4.128 .67 90 3640 5230 66 75 239 248 0 1281 35 1247 2.157 1332 1297 .464 2.514 1.109 1.33 1.109
14 146 268 75 55 71 213 86 216 83 82 11 161 0 0 109 224 47 226 35 35 32 14 284 172 .333 3 14.636 2.88 3.29 9.62 71 280 17.074 .11 100 3780 5230 66 76 253 263 0 168 35 134 1.883 136 101 .531 9.185 .913 3.199 .913
15 206 5273 75 52 131 5221 106 5241 85 60 31 5189 0 0 219 2565 57 52 44 100 37 100 5352 5220 .025 39.855 167.387 61.78 46.494 4.646 83 255 47.58 .41 100 3920 5230 66 76 267 277 0 3309 33 3276 25.01 3289 3256 .04 105.041 4.644 6.715 4.644
16 20249 19569 74 53 20175 19516 16472 12581 82 59 16398 12528 0 0 18830 18218 50 42 98 100 96 100 39691 28926 1.034 .967 .764 1.121 1.015 2.032 118 382 .966 .97 120 4070 5230 65 77 281 293 0 12280 33 12247 .607 7895 7862 1.647 .479 -.72 -1.061 -.72
17 1277 3545 74 52 1203 3493 1209 3834 83 59 1135 3782 0 0 841 1880 40 45 95 98 92 98 4696 4917 .344 2.904 3.332 3.166 3.293 2.877 69 203 3.265 .76 90 4220 5230 66 75 297 306 0 2225 33 2192 1.822 2406 2373 .549 2.091 .866 1.064 .866
18 344 524 74 51 270 473 219 491 78 59 145 440 0 0 295 322 29 49 78 94 69 92 743 585 .571 1.752 3.034 2.614 2.087 5.298 56 218 1.781 .54 90 4370 5230 66 75 312 321 0 329 32 297 1.099 308 276 .91 1.904 .137 .929 .137
19 1445 2298 74 55 1371 2243 1349 2364 78 62 1275 2309 0 0 937 1260 33 48 92 100 92 97 3614 3584 .611 1.636 1.811 1.997 1.489 3.383 68 239 1.656 .82 90 4510 5220 65 74 326 335 0 1442 35 1408 1.027 1483 1449 .974 1.136 .038 .185 .038
20 1019 1453 73 55 946 1398 767 1089 80 63 694 1034 0 0 846 1157 40 53 91 98 90 98 2344 1728 .677 1.478 1.49 1.769 1.633 2.857 80 346 1.792 .58 110 4660 5230 65 76 340 351 0 912 35 877 .927 683 649 1.078 .935 -.109 -.097 -.109

Total number of rows: 41472

Table truncated, full table size 9169 Kbytes.




Supplementary data files not provided
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