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Sample GSM40674 Query DataSets for GSM40674
Status Public on Jan 27, 2006
Title expression array - GBM25
Sample type RNA
 
Channel 1
Source name Cy3: Human Common Reference
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5: GBM25
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: tumor, Brain
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-10/56905
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 = 19:51:49; Parameter PMT Volts = 560; Parameter Scan Date = 2004-10-05; Parameter Pixel Size = 10; Parameter Laser on time = 11079; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.45; 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 = 19:51:49; Parameter PMT Volts = 660; Parameter Scan Date = 2004-10-05; Parameter Pixel Size = 10; Parameter Laser on time = 184684; 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) [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
1 364 143 98 54 266 89 391 104 124 62 293 50 0 0 152 98 103 34 82 60 67 40 355 343 2.989 .335 .171 .229 .225 5.577 40 106 .186 .32 60 1690 5660 70 76 48 54 0 90 34 56 .21 65 31 4.765 .107 -2.253 -3.224 -2.253
2 3583 17608 94 53 3489 17555 499 3204 112 60 405 3151 0 3 4979 23219 82 32 84 100 69 100 21044 3556 .199 5.032 7.78 7.292 5.863 2.303 121 438 4.852 .98 120 1830 5660 67 79 59 71 0 11044 33 11011 3.156 2010 1976 .317 4.88 1.658 2.287 1.658
3 543 249 93 53 450 196 367 177 104 58 274 124 0 0 381 225 56 23 97 83 83 77 646 398 2.296 .436 .453 .387 .396 3.995 36 167 .341 .54 70 1980 5660 69 76 76 83 0 156 33 123 .273 111 78 3.661 .284 -1.872 -1.817 -1.872
4 449 115 94 54 355 61 391 80 98 73 297 26 0 0 286 86 32 134 100 13 92 2 416 323 5.82 .172 .088 .12 .088 3.73 38 175 .142 .54 70 2130 5670 70 77 91 98 0 72 34 38 .108 50 16 9.279 .055 -3.214 -4.187 -3.214
5 262 132 92 53 170 79 231 70 93 58 139 17 0 0 101 190 23 25 96 36 93 27 249 156 2.152 .465 .122 .243 .222 4.739 33 134 1.574 .32 60 2270 5650 69 75 106 112 0 83 33 50 .291 44 11 3.431 .077 -1.779 -3.704 -1.779
6 394 142 92 54 302 88 333 85 96 63 241 31 0 0 189 139 28 54 100 44 96 24 390 272 3.432 .291 .129 .196 .233 2.834 29 154 .433 .77 60 2420 5660 70 76 121 127 0 89 34 55 .183 53 19 5.472 .081 -2.452 -3.632 -2.452
7 322 175 98 56 224 119 316 111 104 57 218 55 0 0 136 168 33 16 96 61 88 57 343 273 1.882 .531 .252 .551 .792 4.825 26 70 .691 .37 50 2560 5650 69 74 135 140 0 110 35 75 .333 70 34 3.001 .158 -1.586 -2.66 -1.586
8 355 153 91 51 264 102 329 137 102 55 238 86 0 0 172 70 56 18 88 96 76 80 366 324 2.588 .386 .361 .424 .309 3.143 26 137 .24 .46 60 2710 5670 71 77 150 156 0 96 32 64 .242 86 54 4.127 .227 -2.045 -2.142 -2.045
9 730 661 93 53 637 608 703 614 103 56 610 561 0 0 327 388 54 19 100 98 94 98 1245 1171 1.048 .954 .92 .816 .837 2.971 56 239 1.034 .69 80 2850 5650 68 76 163 171 0 415 33 381 .599 385 352 1.67 .577 -.74 -.794 -.74
10 417 307 92 55 325 252 393 270 97 65 301 215 0 0 257 189 34 52 95 85 89 71 577 516 1.29 .775 .714 .679 .756 4.073 64 295 .61 .55 100 3000 5650 67 77 177 187 0 193 34 158 .486 169 135 2.056 .448 -1.04 -1.158 -1.04
11 1821 2165 90 55 1731 2110 1938 2212 94 71 1848 2157 0 0 1118 1363 29 60 97 100 94 100 3841 4005 .82 1.219 1.167 1.341 1.253 1.894 74 282 1.241 .9 100 3140 5650 67 77 191 201 0 1358 34 1323 .765 1387 1353 1.308 .732 -.387 -.45 -.387
12 5615 17371 90 52 5525 17319 5653 18903 99 58 5563 18851 0 0 4030 12001 48 28 93 100 88 100 22844 24414 .319 3.135 3.389 3.85 3.022 2.746 88 365 3.124 .98 110 3290 5650 66 77 205 216 0 10895 33 10863 1.966 11856 11824 .509 2.125 .975 1.088 .975
13 863 1692 89 53 774 1639 756 1719 89 61 667 1666 0 0 507 884 22 35 98 100 98 100 2413 2333 .472 2.118 2.498 2.218 2.308 2.085 65 196 2.31 .78 80 3440 5650 68 76 222 230 0 1061 33 1028 1.328 1078 1045 .753 1.567 .409 .648 .409
14 156 689 85 57 71 632 118 659 91 70 33 602 0 0 101 350 46 51 40 98 27 98 703 635 .112 8.901 18.242 12.143 10.692 5.021 65 209 14.589 .34 80 3570 5650 68 76 235 243 0 432 36 396 5.583 413 378 .179 11.442 2.481 3.516 2.481
15 225 1677 86 55 139 1622 170 1711 90 65 84 1656 0 0 179 724 25 37 68 100 60 100 1761 1740 .086 11.669 19.714 18.852 15.75 3.68 70 183 14.412 .48 80 3730 5650 68 76 251 259 0 1052 34 1017 7.319 1073 1039 .137 12.365 2.872 3.628 2.872
16 24844 14219 90 54 24754 14165 19414 9991 94 64 19324 9937 0 0 22477 12776 37 45 100 100 100 99 38919 29261 1.748 .572 .514 .674 .594 1.864 102 320 .565 .98 110 3880 5650 66 77 264 275 0 8918 34 8884 .359 6266 6233 2.786 .323 -1.478 -1.632 -1.478
17 1503 2814 87 54 1416 2760 1465 2949 94 60 1378 2895 0 0 877 1250 45 33 97 100 97 100 4176 4273 .513 1.949 2.101 2.249 2.149 1.974 69 202 1.899 .88 90 4020 5650 67 76 279 288 0 1765 34 1731 1.223 1850 1816 .818 1.318 .29 .398 .29
18 313 2163 90 54 223 2109 274 1989 94 60 184 1935 0 0 240 942 37 30 83 100 71 100 2332 2119 .106 9.457 10.516 13.49 11.956 3.79 67 226 13.826 .46 90 4170 5650 67 76 294 303 0 1357 34 1323 5.932 1248 1214 .169 6.596 2.568 2.722 2.568
19 1481 1950 87 55 1394 1895 1267 2092 94 58 1180 2037 0 0 988 1042 48 17 98 100 97 100 3289 3217 .736 1.359 1.726 1.571 1.607 2.2 71 216 1.297 .83 90 4320 5650 67 76 309 318 0 1223 34 1189 .853 1312 1278 1.173 1.083 -.23 .115 -.23
20 1081 1625 86 57 995 1568 1038 1634 92 59 952 1577 0 0 663 856 43 20 94 100 94 100 2563 2529 .635 1.576 1.657 1.876 1.592 2.746 76 293 1.588 .83 100 4460 5650 67 77 323 333 0 1019 36 983 .988 1025 989 1.012 1.039 -.017 .055 -.017

Total number of rows: 41472

Table truncated, full table size 9211 Kbytes.




Supplementary data files not provided
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