NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM40693 Query DataSets for GSM40693
Status Public on Jan 27, 2006
Title expression array - GBM7
Sample type RNA
 
Channel 1
Source name Cy3: Human Common Reference
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5: GBM7
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: tumor, Brain
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-10/56912
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 = 30.90; Parameter Scan Time = 18:49:43; Parameter PMT Volts = 560; Parameter Scan Date = 2004-10-05; Parameter Pixel Size = 10; Parameter Laser on time = 11018; 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 = 30.90; Parameter Scan Time = 18:49:43; Parameter PMT Volts = 660; Parameter Scan Date = 2004-10-05; Parameter Pixel Size = 10; Parameter Laser on time = 184622; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.55; 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
1 471 246 86 56 385 190 464 160 101 72 378 104 0 0 138 304 57 81 97 64 97 28 575 482 2.026 .494 .275 .251 .279 4.566 42 242 .933 .39 80 1930 5490 73 81 49 57 0 151 34 116 .302 98 64 3.308 .169 -1.726 -2.569 -1.726
2 5355 19381 88 53 5267 19328 620 1969 96 61 532 1916 0 9 7378 25192 51 57 85 100 75 100 24595 2448 .273 3.67 3.602 5.55 4.287 3.061 133 510 3.567 .97 130 2070 5490 70 83 60 73 0 11871 32 11838 2.248 1206 1174 .445 2.206 1.168 1.141 1.168
3 804 412 84 52 720 360 615 309 107 55 531 257 0 0 558 386 141 17 88 97 76 94 1080 788 2 .5 .484 .519 .386 4.244 34 108 .407 .53 60 2220 5490 74 80 79 85 0 252 32 220 .306 189 157 3.265 .296 -1.707 -1.754 -1.707
4 757 341 87 53 670 288 748 212 106 67 661 159 0 0 467 272 118 57 88 86 82 66 958 820 2.326 .43 .241 .341 .373 4.509 51 296 .402 .7 90 2360 5490 72 81 91 100 0 209 32 176 .263 130 97 3.798 .147 -1.925 -2.763 -1.925
5 263 180 91 54 172 126 227 78 105 63 136 24 0 0 150 215 64 39 89 45 56 37 298 160 1.365 .733 .176 .415 .544 6.964 37 191 1.488 .25 70 2510 5480 72 79 107 114 0 110 33 77 .449 48 15 2.229 .108 -1.156 -3.21 -1.156
6 665 234 88 52 577 182 532 98 100 60 444 46 0 0 416 335 70 35 100 52 100 38 759 490 3.17 .315 .104 .134 .132 4.969 34 150 .408 .55 60 2650 5490 74 80 122 128 0 143 32 111 .193 60 28 5.176 .063 -2.372 -3.978 -2.372
7 388 284 87 53 301 231 330 228 91 66 243 175 0 0 210 237 32 47 100 72 96 63 532 418 1.303 .767 .72 .594 .782 5.2 33 145 .734 .38 60 2790 5500 75 81 136 142 0 174 32 141 .47 140 107 2.127 .441 -1.089 -1.181 -1.089
8 460 603 87 53 373 550 300 292 94 63 213 239 0 0 377 707 32 42 82 82 75 75 923 452 .678 1.475 1.122 1.163 1.334 6.011 41 178 2.105 .71 70 2940 5490 73 80 150 157 0 369 32 337 .903 179 146 1.107 .687 -.147 -.541 -.147
9 1160 980 84 51 1076 929 894 905 94 56 810 854 0 0 917 636 75 26 93 98 90 98 2005 1664 1.158 .863 1.054 .99 1.05 3.874 66 241 .649 .54 90 3090 5490 72 81 164 173 0 600 31 569 .529 554 523 1.891 .646 -.919 -.631 -.919
10 562 566 88 53 474 513 436 412 103 61 348 359 0 0 439 487 97 38 80 93 66 90 987 707 .924 1.082 1.032 1.168 1.128 4.593 75 285 1.162 .43 100 3240 5490 72 82 179 189 0 347 32 314 .663 252 220 1.509 .632 -.593 -.662 -.593
11 3373 5677 84 53 3289 5624 3537 6012 93 64 3453 5959 0 0 1716 2844 73 53 95 100 94 100 8913 9412 .585 1.71 1.726 1.921 1.734 2.405 73 229 1.788 .9 90 3380 5480 71 80 193 202 0 3477 32 3445 1.047 3682 3650 .955 1.057 .067 .08 .067
12 9759 22129 86 53 9673 22076 12186 27731 100 63 12100 27678 0 0 6607 13823 87 55 96 100 92 100 31749 39778 .438 2.282 2.287 2.994 2.361 2.719 88 337 2.31 .94 110 3530 5490 71 82 207 218 0 13554 32 13521 1.398 16985 16952 .715 1.401 .483 .486 .483
13 1343 2845 85 53 1258 2792 1132 2804 98 59 1047 2751 0 0 1057 1410 82 26 93 100 88 100 4050 3798 .451 2.219 2.628 2.961 2.383 2.757 76 291 2.136 .77 100 3680 5490 72 82 223 233 0 1743 32 1710 1.359 1717 1685 .736 1.609 .443 .686 .443
14 208 1289 83 55 125 1234 109 1266 89 71 26 1211 0 0 188 645 38 101 43 100 36 100 1359 1237 .101 9.872 46.577 16.444 15.188 5.657 79 298 14.451 .36 100 3820 5490 72 82 237 247 0 789 34 756 6.046 775 742 .165 28.528 2.596 4.834 2.596
15 256 2882 83 54 173 2828 179 2676 93 66 96 2622 0 0 220 1172 52 60 57 100 47 100 3001 2718 .061 16.347 27.313 24.099 18.963 4.129 71 207 23.215 .4 90 3960 5490 72 81 251 260 0 1765 33 1732 10.012 1639 1606 .1 16.729 3.324 4.064 3.324
16 33754 26484 85 54 33669 26430 32251 28800 94 60 32166 28746 11 0 28682 21401 55 32 100 100 100 100 60099 60912 1.274 .785 .894 .871 .785 2.099 106 409 .759 .97 120 4120 5490 71 83 266 278 0 16221 33 16188 .481 17640 17607 2.08 .547 -1.056 -.869 -1.056
17 1970 5846 83 53 1887 5793 1975 6193 91 61 1892 6140 0 0 1309 3257 43 36 91 100 90 100 7680 8032 .326 3.07 3.245 4.213 3.32 3.587 81 255 3.366 .81 100 4260 5490 72 82 281 291 0 3581 32 3548 1.88 3793 3761 .532 1.988 .911 .991 .911
18 483 2673 81 53 402 2620 385 2763 88 60 304 2710 0 0 416 999 40 32 87 100 76 100 3022 3014 .153 6.517 8.914 10.324 8.928 3.383 71 201 7.425 .58 90 4400 5480 71 80 295 304 0 1637 32 1605 3.992 1692 1660 .251 5.46 1.997 2.449 1.997
19 2481 4000 81 55 2400 3945 2410 3862 86 71 2329 3807 0 0 1585 2190 35 88 100 98 100 97 6345 6136 .608 1.644 1.635 1.649 1.641 2.599 72 277 1.704 .81 100 4550 5490 72 82 310 320 0 2450 34 2416 1.007 2365 2332 .993 1.001 .01 .002 .01
20 1915 2363 82 54 1833 2309 1730 2474 89 70 1648 2420 0 0 1284 1257 46 95 97 98 97 98 4142 4068 .794 1.26 1.468 1.31 1.285 2.939 79 339 1.189 .83 110 4690 5490 71 82 323 334 0 1447 33 1414 .772 1515 1482 1.296 .899 -.374 -.153 -.374

Total number of rows: 41472

Table truncated, full table size 9254 Kbytes.




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