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Sample GSM40687 Query DataSets for GSM40687
Status Public on Jan 27, 2006
Title expression array - O4
Sample type RNA
 
Channel 1
Source name Cy3: Human Common Reference
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5: O4
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: tumor, Brain
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-10/56948
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 = 30.94; Parameter Scan Time = 21:03:30; Parameter PMT Volts = 570; Parameter Scan Date = 2004-10-12; Parameter Pixel Size = 10; Parameter Laser on time = 13147; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.44; 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 = 30.94; Parameter Scan Time = 21:03:30; Parameter PMT Volts = 670; Parameter Scan Date = 2004-10-12; Parameter Pixel Size = 10; Parameter Laser on time = 186752; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.58; 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
1 403 138 123 53 280 85 414 73 135 71 291 20 0 0 60 241 74 125 100 10 96 10 365 311 3.294 .304 .069 .083 .079 5.506 30 156 1.323 .23 60 1620 5460 55 61 47 53 0 83 32 51 .182 44 12 5.481 .041 -2.455 -4.598 -2.455
2 14023 584 116 55 13907 529 14594 469 134 72 14478 414 0 0 11277 508 87 118 98 70 98 60 14436 14892 26.289 .038 .029 .034 .036 2.356 58 269 .035 .81 80 1760 5460 54 62 60 68 0 351 33 318 .023 282 249 43.745 .017 -5.451 -5.863 -5.451
3 705 570 109 51 596 519 589 518 126 60 480 467 0 0 503 286 84 51 100 100 92 96 1115 947 1.148 .871 .973 .906 1.051 2.345 26 160 .649 .64 60 1910 5460 55 61 76 82 0 343 31 312 .523 311 281 1.911 .585 -.934 -.774 -.934
4 449 159 111 54 338 105 352 84 131 59 241 30 0 0 315 192 98 29 76 51 53 39 443 271 3.219 .311 .124 .201 .211 6.205 43 179 .172 .28 70 2060 5470 55 62 90 97 0 96 32 63 .187 50 18 5.357 .075 -2.421 -3.741 -2.421
5 264 74 111 53 153 21 228 62 118 57 117 9 0 0 117 61 48 26 95 16 67 6 174 126 7.286 .137 .077 .138 .1 4.139 43 246 .028 .05 80 2210 5470 55 63 105 113 0 44 32 13 .082 37 5 12.123 .046 -3.6 -4.435 -3.6
6 382 67 111 53 271 14 373 63 116 60 262 10 0 0 100 23 33 45 100 10 100 3 285 272 19.357 .052 .038 .06 .061 2.521 30 153 -.022 -.05 60 2350 5460 55 61 120 126 0 40 32 8 .031 38 6 32.21 .023 -5.009 -5.446 -5.009
7 358 322 111 58 247 264 344 125 113 66 233 67 0 0 143 367 28 54 100 56 91 47 511 300 .936 1.069 .288 .539 .686 6.327 23 169 11.528 .18 60 2500 5460 55 61 135 141 0 194 35 159 .642 75 40 1.557 .173 -.639 -2.533 -.639
8 368 1619 115 56 253 1563 385 1051 126 63 270 995 0 0 131 2223 46 35 92 100 85 100 1816 1265 .162 6.178 3.685 4.785 4.603 2.363 27 135 18.334 .57 60 2650 5460 55 61 150 156 0 973 34 939 3.713 632 598 .269 2.215 1.892 1.147 1.892
9 579 747 111 52 468 695 492 615 115 58 381 563 0 0 416 582 33 26 93 98 86 94 1163 944 .673 1.485 1.478 1.756 1.785 4.51 59 266 2.061 .46 90 2770 5450 52 61 160 169 0 449 31 418 .892 370 338 1.121 .888 -.164 -.171 -.164
10 873 319 108 51 765 268 781 226 114 57 673 175 0 0 614 374 37 22 97 86 95 71 1033 848 2.854 .35 .26 .264 .241 7.427 67 245 .15 .24 90 2910 5450 52 61 174 183 0 192 31 161 .211 136 105 4.75 .156 -2.248 -2.678 -2.248
11 3716 4752 109 53 3607 4699 3863 4432 116 60 3754 4379 0 0 1624 1839 60 41 100 100 100 100 8306 8133 .768 1.303 1.166 1.373 1.29 1.682 69 259 1.297 .9 90 3060 5450 52 61 189 198 0 2856 32 2824 .783 2663 2632 1.277 .701 -.353 -.512 -.353
12 15322 24170 108 54 15214 24116 18869 28507 114 61 18761 28453 0 0 9637 14379 53 53 98 100 97 100 39330 47214 .631 1.585 1.517 1.952 1.628 2.377 78 242 1.573 .97 90 3210 5450 52 61 204 213 0 14525 32 14493 .953 17132 17099 1.05 .911 -.07 -.134 -.07
13 2098 5093 107 54 1991 5039 1971 4713 112 62 1864 4659 0 0 928 2009 37 48 100 100 100 100 7030 6523 .395 2.531 2.499 2.707 2.673 1.841 58 219 2.775 .84 80 3360 5450 53 61 220 228 0 3061 32 3028 1.521 2832 2800 .657 1.502 .605 .587 .605
14 240 3576 109 54 131 3522 140 3257 111 60 31 3203 0 0 228 1730 44 32 45 100 34 100 3653 3234 .037 26.885 103.323 48.375 42.98 5.797 87 330 29.774 .43 100 3500 5450 52 62 233 243 0 2149 32 2117 16.157 1957 1925 .062 62.093 4.014 5.956 4.014
15 238 825 107 55 131 770 144 622 114 70 37 567 0 0 182 563 50 81 43 100 35 98 901 604 .17 5.878 15.324 6.578 6.992 4.783 65 240 11.425 .32 90 3650 5450 52 61 248 257 0 496 33 463 3.532 374 341 .283 9.209 1.821 3.203 1.821
16 31208 33018 106 57 31102 32961 35383 34515 115 70 35277 34458 3 10 24556 26421 48 94 98 100 98 100 64063 69735 .944 1.06 .977 1.156 1.067 2.749 101 410 1.068 .98 120 3800 5460 52 64 262 274 0 19842 34 19808 .637 20742 20708 1.57 .587 -.651 -.769 -.651
17 2277 2742 104 58 2173 2684 2356 2386 114 75 2252 2328 0 0 1274 1711 53 86 95 100 95 98 4857 4580 .81 1.235 1.034 1.374 1.179 2.306 61 176 1.345 .81 80 3950 5460 54 62 279 287 0 1648 35 1613 .742 1434 1399 1.347 .621 -.43 -.687 -.43
18 693 7836 107 56 586 7780 552 8379 122 70 445 8323 0 0 555 3473 90 78 81 100 68 100 8366 8768 .075 13.276 18.703 23.033 15.296 3.888 70 233 13.17 .74 90 4080 5450 52 61 291 300 0 4709 34 4675 7.979 5035 5002 .125 11.24 2.996 3.491 2.996
19 2337 4278 102 56 2235 4222 1991 3822 116 67 1889 3766 0 0 1537 2533 93 70 98 100 94 100 6457 5655 .529 1.889 1.994 2.042 2.158 2.005 75 275 1.922 .89 100 4240 5460 53 63 307 317 0 2571 34 2537 1.135 2297 2263 .881 1.198 .183 .261 .183
20 3141 3468 104 60 3037 3408 2982 3385 112 65 2878 3325 0 0 2077 1861 62 33 98 100 98 100 6445 6203 .891 1.122 1.155 1.253 1.216 2.276 78 285 1.045 .85 100 4380 5460 53 63 321 331 0 2084 36 2048 .674 2034 1998 1.483 .694 -.568 -.526 -.568

Total number of rows: 41472

Table truncated, full table size 9201 Kbytes.




Supplementary data files not provided
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