NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM40683 Query DataSets for GSM40683
Status Public on Jan 27, 2006
Title expression array - GBM3
Sample type RNA
 
Channel 1
Source name Cy3: Human Common Reference
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5: GBM3
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: tumor, Brain
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-10/56944
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 = 31.30; Parameter Scan Time = 21:54:05; Parameter PMT Volts = 560; Parameter Scan Date = 2004-10-12; Parameter Pixel Size = 10; Parameter Laser on time = 13197; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.43; 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 = 31.30; Parameter Scan Time = 21:54:05; Parameter PMT Volts = 670; Parameter Scan Date = 2004-10-12; Parameter Pixel Size = 10; Parameter Laser on time = 186802; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.57; 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
1 292 771 110 54 182 717 288 671 116 64 178 617 0 0 79 482 46 41 98 96 82 94 899 795 .254 3.94 3.466 3.053 3.709 2.855 52 312 5.719 .72 90 1660 5790 62 71 57 66 0 562 39 523 2.873 489 450 .348 2.528 1.523 1.338 1.523
2 5411 24536 105 55 5306 24481 2108 11824 110 63 2003 11769 0 5 6089 25362 34 37 91 100 89 99 29787 13772 .217 4.614 5.876 5.841 5.11 2.36 101 470 4.432 .98 120 1800 5790 61 73 70 82 0 17894 40 17854 3.365 8623 8583 .297 4.285 1.751 2.099 1.751
3 359 324 108 55 251 269 292 199 118 76 184 144 0 0 204 303 52 81 91 70 78 48 520 328 .933 1.072 .783 .822 .939 2.577 47 148 1.378 .78 70 1950 5790 63 70 87 94 0 236 40 196 .782 145 105 1.279 .571 -.356 -.809 -.356
4 328 78 105 57 223 21 300 67 108 71 195 10 0 0 130 47 28 72 97 8 94 2 244 205 10.619 .094 .051 .137 .142 2.959 37 196 -1 -1 70 2100 5780 62 69 102 109 0 57 42 15 .069 49 7 14.561 .037 -3.864 -4.741 -3.864
5 333 126 102 53 231 73 236 119 109 59 134 66 0 0 316 73 30 29 94 58 89 51 304 200 3.164 .316 .493 .303 .427 5.709 39 123 .089 .32 60 2250 5780 63 69 118 124 0 92 39 53 .23 87 48 4.339 .359 -2.117 -1.477 -2.117
6 338 74 100 56 238 18 294 67 104 64 194 11 0 0 128 29 29 31 100 28 100 10 256 205 13.222 .076 .057 .094 .094 3.601 38 168 .043 .15 70 2380 5790 63 70 130 137 0 54 41 13 .055 49 8 18.13 .041 -4.18 -4.596 -4.18
7 282 79 97 59 185 20 260 67 104 61 163 8 0 0 92 39 36 17 100 36 96 23 205 171 9.25 .108 .049 .113 .127 3.872 30 145 .057 .19 60 2540 5800 65 71 147 153 0 58 43 15 .079 49 6 12.684 .036 -3.665 -4.804 -3.665
8 289 198 99 56 190 142 266 145 105 60 167 89 0 0 116 199 35 25 97 82 90 67 332 256 1.338 .747 .533 .518 .554 5.118 40 222 1.651 .24 80 2690 5780 62 70 161 169 0 144 41 104 .545 106 65 1.835 .389 -.876 -1.363 -.876
9 470 510 102 56 368 454 403 420 105 60 301 364 0 0 240 382 27 23 98 100 96 100 822 665 .811 1.234 1.209 1.246 1.27 2.8 79 251 1.611 .65 100 2820 5790 62 72 173 183 0 372 41 331 .9 306 265 1.111 .882 -.152 -.181 -.152
10 513 143 100 57 413 86 435 106 104 64 335 49 0 0 294 110 24 34 98 60 98 41 499 384 4.802 .208 .146 .168 .148 4.688 73 229 .107 .32 100 2960 5790 62 72 187 197 0 104 42 63 .152 77 36 6.585 .107 -2.719 -3.229 -2.719
11 2226 1866 100 56 2126 1810 2082 1851 106 62 1982 1795 0 0 954 974 32 25 100 100 100 98 3936 3777 1.175 .851 .906 .769 .817 2.089 80 274 .87 .85 100 3110 5790 62 72 202 212 0 1361 41 1320 .621 1350 1309 1.611 .66 -.688 -.598 -.688
12 9452 26332 99 57 9353 26275 9829 27585 103 60 9730 27528 0 0 5540 15454 28 21 97 100 97 100 35628 37258 .356 2.809 2.829 3.017 2.882 1.902 89 280 2.861 .97 100 3260 5790 62 72 217 227 0 19203 42 19162 2.049 20117 20076 .488 2.063 1.035 1.045 1.035
13 1373 4030 97 56 1276 3974 1164 4066 107 65 1067 4010 0 0 826 1640 41 39 100 100 100 100 5250 5077 .321 3.114 3.758 3.383 3.506 1.887 68 217 3.279 .79 90 3400 5790 62 71 231 240 0 2939 41 2898 2.271 2965 2924 .44 2.741 1.184 1.455 1.184
14 264 200 97 55 167 145 209 135 107 59 112 80 0 0 181 207 46 21 63 72 54 57 312 192 1.152 .868 .714 .989 1.083 14.524 33 251 .748 .05 90 3550 5780 61 70 246 255 0 146 40 106 .633 98 58 1.579 .521 -.659 -.941 -.659
15 204 14746 99 58 105 14688 129 16203 105 63 30 16145 0 0 185 5390 33 28 47 100 34 100 14793 16175 .007 139.886 538.167 280.123 294.368 4.346 88 277 151.669 .42 100 3700 5780 61 71 261 271 0 10754 42 10712 102.016 11817 11774 .01 392.475 6.673 8.616 6.673
16 33891 23347 100 58 33791 23289 37474 25005 105 66 37374 24947 0 0 17649 12547 32 33 100 100 100 100 57080 62321 1.451 .689 .667 .688 .7 1.329 83 261 .692 .99 100 3840 5790 62 72 275 285 0 17027 42 16984 .503 18236 18193 1.99 .487 -.992 -1.039 -.992
17 1749 3441 97 56 1652 3385 1621 3227 101 66 1524 3171 0 0 719 1700 31 40 100 100 98 100 5037 4695 .488 2.049 2.081 2.019 2.033 1.743 74 216 2.245 .92 90 3990 5780 61 70 290 299 0 2509 41 2469 1.494 2353 2313 .669 1.517 .579 .602 .579
18 453 1777 98 58 355 1719 417 1612 105 70 319 1554 0 0 225 976 58 47 93 100 87 100 2074 1873 .207 4.842 4.871 5.446 5.046 2.871 73 247 6.4 .71 100 4140 5780 61 71 305 315 0 1296 42 1254 3.531 1176 1133 .283 3.553 1.82 1.829 1.82
19 1748 1780 102 60 1646 1720 1688 1626 113 79 1586 1566 0 0 913 1048 54 93 100 100 98 96 3366 3152 .957 1.045 .987 1.008 1.047 2.103 84 167 1.086 .87 90 4270 5780 61 70 318 327 0 1298 44 1254 .762 1186 1142 1.312 .72 -.392 -.474 -.392
20 1978 2430 102 58 1876 2372 2027 2390 109 64 1925 2332 0 0 937 1300 46 28 100 100 100 100 4248 4257 .791 1.264 1.211 1.234 1.235 1.703 82 285 1.352 .85 100 4420 5780 61 71 333 343 0 1772 42 1730 .922 1743 1701 1.084 .883 -.117 -.179 -.117

Total number of rows: 41472

Table truncated, full table size 9150 Kbytes.




Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap