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Sample GSM40671 Query DataSets for GSM40671
Status Public on Jan 27, 2006
Title expression array - GBM5
Sample type RNA
 
Channel 1
Source name Cy3: Human Common Reference
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5: GBM5
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: tumor, Brain
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-09/55568
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 = 30.63; Parameter Scan Time = 18:58:06; Parameter PMT Volts = 550; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 6563; 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 = 30.63; Parameter Scan Time = 18:58:06; Parameter PMT Volts = 660; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 180104; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.56; 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
1 421 353 101 52 320 301 429 305 101 57 328 253 0 0 134 207 21 19 100 97 100 94 621 581 1.063 .941 .771 .727 1.067 2.837 38 127 1.144 .72 60 1740 5290 86 92 59 65 0 179 26 153 .478 155 128 2.093 .392 -1.066 -1.352 -1.066
2 3423 9563 96 55 3327 9508 432 1389 100 61 336 1334 0 0 4674 12950 27 30 97 100 97 100 12835 1670 .35 2.858 3.97 3.217 2.88 2.222 123 458 2.837 .98 120 1880 5300 84 96 70 82 0 4856 28 4829 1.451 705 677 .689 2.016 .537 1.012 .537
3 632 607 95 60 537 547 521 519 99 69 426 459 0 0 504 508 32 37 92 94 78 92 1084 885 .982 1.019 1.077 1.205 1.327 2.618 38 158 1.022 .72 70 2040 5290 85 92 88 95 0 308 30 278 .517 264 233 1.933 .547 -.951 -.87 -.951
4 457 231 94 55 363 176 400 141 98 62 306 86 0 0 286 217 28 31 94 73 92 57 539 392 2.063 .485 .281 .378 .471 4.711 52 367 .518 .66 100 2180 5300 85 95 101 111 0 117 28 89 .246 72 44 4.061 .143 -2.022 -2.809 -2.022
5 229 184 96 56 133 128 216 161 100 70 120 105 0 0 82 140 23 57 100 62 97 40 261 225 1.039 .962 .875 .61 1.05 5.206 37 175 1.933 .33 70 2330 5290 85 92 117 124 0 93 28 65 .489 82 53 2.046 .444 -1.033 -1.17 -1.033
6 453 158 96 56 357 102 444 100 99 64 348 44 0 0 161 130 20 34 100 59 100 40 459 392 3.5 .286 .126 .175 .205 3.177 27 159 .332 .63 60 2470 5290 86 92 132 138 0 80 28 52 .145 51 22 6.892 .064 -2.785 -3.961 -2.785
7 282 113 97 61 185 52 271 80 106 72 174 19 0 0 112 108 43 43 91 28 71 20 237 193 3.558 .281 .109 .256 .209 5.165 35 192 .173 .21 70 2620 5290 85 92 146 153 0 57 31 26 .143 41 10 7.006 .055 -2.809 -4.173 -2.809
8 222 205 95 56 127 149 149 118 102 64 54 62 0 0 162 220 36 32 61 73 44 48 276 116 .852 1.173 1.148 1.31 1.14 5.149 52 210 1.387 .7 80 2770 5280 84 92 161 169 0 104 28 76 .596 60 31 1.678 .583 -.747 -.778 -.747
9 785 1107 94 58 691 1049 760 987 102 73 666 929 0 0 434 608 33 86 96 100 93 98 1740 1595 .659 1.518 1.395 1.776 1.403 2.592 63 241 1.622 .81 90 2910 5290 84 93 174 183 0 562 29 533 .771 501 472 1.297 .708 -.375 -.497 -.375
10 367 287 94 59 273 228 310 204 100 74 216 145 0 0 187 227 32 90 93 67 91 46 501 361 1.197 .835 .671 .684 .67 4.676 62 219 1.032 .47 90 3060 5300 85 94 189 198 0 146 30 116 .424 104 74 2.358 .341 -1.237 -1.553 -1.237
11 1873 3600 93 53 1780 3547 1946 3871 101 62 1853 3818 0 0 1166 2353 35 31 92 100 92 98 5327 5671 .502 1.993 2.06 2.259 2.183 2.116 75 210 2.098 .93 90 3200 5290 84 93 203 212 0 1828 27 1801 1.012 1966 1939 .988 1.046 .017 .065 .017
12 4031 17518 94 60 3937 17458 2165 9026 102 80 2071 8966 0 0 4196 18193 43 71 87 98 80 98 21395 11037 .226 4.434 4.329 5.911 4.603 2.663 108 453 4.434 .99 130 3340 5300 83 96 215 228 0 8896 30 8866 2.252 4584 4553 .444 2.199 1.171 1.137 1.171
13 762 3143 95 60 667 3083 738 3200 107 68 643 3140 0 0 359 1511 54 33 100 100 100 98 3750 3783 .216 4.622 4.883 4.475 4.733 2.181 66 194 5.111 .87 90 3490 5290 84 93 232 241 0 1596 30 1566 2.347 1625 1595 .426 2.48 1.231 1.31 1.231
14 187 542 91 61 96 481 155 347 101 70 64 286 0 0 112 474 49 45 53 94 37 90 577 350 .2 5.01 4.469 4.742 4.063 5.291 75 292 14.344 .27 100 3630 5290 84 94 246 256 0 275 31 244 2.544 176 145 .393 2.269 1.347 1.182 1.347
15 236 7286 89 61 147 7225 212 8101 101 82 123 8040 0 0 131 3969 55 67 70 100 54 100 7372 8163 .02 49.15 65.366 58.672 53.519 2.707 77 201 55.24 .68 90 3780 5290 84 93 261 270 0 3700 31 3669 24.96 4114 4083 .04 33.195 4.642 5.053 4.642
16 22665 20881 91 59 22574 20822 9782 11163 96 96 9691 11104 0 0 23457 21201 30 283 100 98 100 90 43396 20795 1.084 .922 1.146 1.035 .954 1.429 113 397 .91 .99 120 3930 5290 83 95 275 287 0 10604 30 10574 .468 5669 5639 2.135 .582 -1.094 -.781 -1.094
17 1536 5901 92 59 1444 5842 1449 6051 99 72 1357 5992 0 0 979 3027 37 48 95 100 93 100 7286 7349 .247 4.046 4.416 5.056 4.565 2.046 64 188 4.189 .87 80 4080 5290 85 93 292 300 0 2997 30 2967 2.055 3073 3043 .487 2.242 1.039 1.165 1.039
18 313 1464 89 60 224 1404 262 1248 97 70 173 1188 0 0 201 825 34 37 81 100 70 100 1628 1361 .16 6.268 6.867 8.454 7.894 3.634 65 195 9.602 .52 80 4220 5290 85 93 306 314 0 743 30 713 3.183 634 603 .314 3.487 1.67 1.802 1.67
19 1559 2840 90 59 1469 2781 1584 2989 96 83 1494 2930 0 0 922 1357 26 111 100 100 98 100 4250 4424 .528 1.893 1.961 2.354 1.904 2.062 68 215 1.838 .91 90 4370 5290 84 93 320 329 0 1442 30 1412 .961 1518 1488 1.04 .996 -.057 -.006 -.057
20 1480 2164 94 60 1386 2104 1406 2252 101 72 1312 2192 0 0 792 1015 51 50 98 100 98 100 3490 3504 .659 1.518 1.671 1.64 1.669 1.66 75 309 1.483 .92 100 4510 5290 84 94 334 344 0 1099 30 1068 .771 1144 1113 1.297 .848 -.375 -.237 -.375

Total number of rows: 41472

Table truncated, full table size 9355 Kbytes.




Supplementary data files not provided
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