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Sample GSM40627 Query DataSets for GSM40627
Status Public on Jan 27, 2006
Title expression array MER-TMZ
Sample type RNA
 
Channel 1
Source name Cy3: Universal Human Reference
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5: MER-TMZ
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: tumor, Brain
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-09/55628.gif
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 = 31.45; Parameter Scan Time = 00:03:26; Parameter PMT Volts = 530; Parameter Scan Date = 2004-09-01; Parameter Pixel Size = 10; Parameter Laser on time = 4772; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.53; 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 = 31.45; Parameter Scan Time = 00:03:26; Parameter PMT Volts = 650; Parameter Scan Date = 2004-09-01; Parameter Pixel Size = 10; Parameter Laser on time = 178055; 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 24, 2006
Contact name Markus Bredel
E-mail(s) mbredel@stanford.edu
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 GPL1831
Series (1)
GSE2221 Drug resistance in glioblastoma

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
1 258 191 63 58 195 133 137 76 88 88 74 18 0 0 355 261 83 94 46 32 23 19 328 92 1.466 .682 .243 .627 .629 4.685 52 248 .726 .61 80 1930 5180 82 90 77 85 -50 101 31 70 .359 40 9 2.785 .128 -2.965 -1.478
2 2213 213 65 60 2148 153 2110 126 101 108 2045 66 0 0 862 233 99 133 100 28 100 17 2301 2111 14.039 .071 .032 .038 .032 3.835 145 471 .048 .26 130 2080 5190 80 93 89 102 0 112 32 81 .037 66 35 26.668 .017 -4.737 -5.879 -4.737
3 582 1076 61 53 521 1023 523 1044 81 78 462 991 0 0 316 483 72 102 97 100 92 99 1544 1453 .509 1.964 2.145 2.184 2.057 2.457 144 473 2.061 .6 130 2230 5190 80 93 104 117 0 566 28 539 1.034 550 522 .967 1.129 .048 .175 .048
4 106 105 60 56 46 49 90 61 75 78 30 5 0 0 63 101 59 93 21 21 7 11 95 35 .939 1.065 .167 1.311 1.375 7.385 52 204 1.754 .13 80 2370 5180 82 90 121 129 -50 55 29 26 .561 32 3 1.783 .088 -3.511 -.835
5 345 156 66 55 279 101 171 113 84 68 105 58 0 0 546 126 67 42 54 54 45 45 380 163 2.762 .362 .552 1.524 .656 10.232 11 61 .154 .51 40 2490 5160 82 86 135 139 0 82 29 53 .191 59 31 5.247 .291 -2.392 -1.782 -2.392
6 169 129 61 52 108 77 129 72 69 65 68 20 0 0 155 138 42 100 61 22 42 11 185 88 1.403 .713 .294 .714 .539 8.649 84 543 .442 .18 130 2650 5180 79 92 146 159 0 68 27 41 .375 38 11 2.664 .155 -1.414 -2.691 -1.414
7 189 177 64 61 125 116 147 108 81 73 83 47 0 0 127 161 62 77 54 45 36 18 241 130 1.078 .928 .566 .972 .747 3.773 11 50 2.656 .19 40 2800 5170 83 87 166 170 0 93 32 61 .489 57 25 2.047 .298 -1.033 -1.746 -1.033
8 158 221 60 55 98 166 126 173 68 65 66 118 0 0 101 150 63 49 57 80 26 57 264 184 .59 1.694 1.788 2.03 1.472 6.297 45 201 3.896 .32 80 2950 5180 82 90 179 187 0 116 29 87 .892 91 62 1.121 .941 -.165 -.087 -.165
9 414 679 61 54 353 625 359 646 92 131 298 592 0 0 282 369 116 269 79 81 61 56 978 890 .565 1.771 1.987 2.039 1.723 3.025 143 889 2.32 .61 170 3110 5200 79 96 190 207 0 357 28 329 .932 340 312 1.073 1.046 -.101 .065 -.101
10 235 403 67 66 168 337 238 348 136 192 171 282 0 0 133 233 165 257 55 55 11 15 505 453 .499 2.006 1.649 2.426 2.193 3.814 52 131 4.101 .25 80 3240 5200 84 92 208 216 -50 212 35 177 1.056 183 148 .947 .868 -.204 .079
11 1135 1229 62 54 1073 1175 932 1154 87 94 870 1100 0 0 613 567 84 131 98 100 97 95 2248 1970 .913 1.095 1.264 1.166 1.216 2.182 149 424 2.093 .64 130 3390 5180 79 92 220 233 0 647 28 619 .576 608 579 1.735 .666 -.795 -.587 -.795
12 4187 12881 62 54 4125 12827 4142 12902 83 96 4080 12848 0 0 1337 3607 72 206 100 100 100 100 16952 16928 .322 3.11 3.149 3.168 3.123 1.396 147 414 3.194 .93 130 3540 5180 79 92 235 248 0 6781 28 6753 1.637 6792 6764 .611 1.658 .711 .729 .711
13 524 2271 62 54 462 2217 423 2138 82 70 361 2084 0 0 440 909 81 60 86 100 76 100 2679 2445 .208 4.799 5.773 7.093 5.959 3.195 150 423 3.274 .92 130 3680 5180 79 92 249 262 0 1196 28 1167 2.526 1126 1097 .396 3.039 1.337 1.604 1.337
14 106 75 63 56 43 19 69 62 73 74 6 6 0 0 91 41 50 64 19 7 19 3 62 12 2.263 .442 1 .827 .512 7.868 52 210 .173 .04 80 3830 5170 81 89 267 275 -50 39 29 10 .233 33 3 4.299 .526 -.926 -2.104
15 156 259 63 54 93 205 93 230 79 93 30 176 0 0 152 171 61 155 32 53 26 26 298 206 .454 2.204 5.867 2.749 2.441 7.591 52 200 4.532 .22 80 3970 5170 81 89 281 289 -50 136 28 108 1.16 121 93 .862 3.088 1.627 .215
16 18025 34519 62 52 17963 34467 17951 34407 69 74 17889 34355 0 0 5196 7235 40 107 100 100 100 100 52430 52244 .521 1.919 1.92 2.03 1.887 1.566 153 512 1.897 .96 140 4120 5180 79 93 293 307 0 18172 27 18145 1.01 18113 18086 .99 1.011 .015 .016 .015
17 896 2370 60 52 836 2318 725 1946 72 69 665 1894 0 0 1321 2407 56 84 96 100 94 100 3154 2559 .361 2.773 2.848 3.416 3.085 2.369 148 368 1.924 .97 130 4260 5180 79 92 307 320 0 1248 27 1220 1.46 1024 997 .685 1.499 .546 .584 .546
18 207 109 60 53 147 56 162 77 86 62 102 24 0 0 157 95 97 42 55 38 28 21 203 126 2.625 .381 .235 .318 .51 4.793 52 144 .132 .15 80 4410 5170 81 89 325 333 -50 57 28 29 .201 41 13 4.986 .124 -3.013 -2.318
19 914 1757 60 52 854 1705 860 1639 77 73 800 1587 0 0 452 608 76 86 99 100 99 100 2559 2387 .501 1.996 1.984 2.195 2.2 1.977 141 367 2.095 .75 130 4560 5180 79 92 337 350 0 925 27 898 1.051 863 835 .951 1.044 .072 .063 .072
20 791 1001 59 53 732 948 657 926 76 86 598 873 0 0 590 472 65 122 97 97 95 96 1680 1471 .772 1.295 1.46 1.484 1.534 2.536 142 476 1.174 .65 140 4710 5180 79 93 352 366 0 527 28 499 .682 487 460 1.467 .769 -.553 -.38 -.553

Total number of rows: 41472

Table truncated, full table size 9176 Kbytes.




Supplementary data files not provided
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