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Sample GSM40710 Query DataSets for GSM40710
Status Public on Jan 27, 2006
Title expression array - GNN1
Sample type RNA
 
Channel 1
Source name Cy3: Human Common Reference
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5: GNN1
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: tumor, Brain
Image: http://genome-www5.stanford.edu/MicroArray/gifs//56954
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 = 30.69; Parameter Scan Time = 20:39:28; Parameter PMT Volts = 570; Parameter Scan Date = 2004-10-12; Parameter Pixel Size = 10; Parameter Laser on time = 13123; 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 = 30.69; Parameter Scan Time = 20:39:28; Parameter PMT Volts = 670; Parameter Scan Date = 2004-10-12; Parameter Pixel Size = 10; Parameter Laser on time = 186727; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.58; 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
1 301 78 108 53 193 25 304 62 113 60 196 9 0 0 76 46 29 28 97 21 93 14 218 205 7.72 .13 .046 .101 .077 4.432 47 270 .073 .2 80 1760 5840 72 80 60 68 0 52 36 17 .087 42 6 11.489 .031 -3.522 -5.018 -3.522
2 5561 335 105 54 5456 281 6210 266 107 61 6105 212 0 0 3260 248 24 32 100 85 100 75 5737 6317 19.416 .052 .035 .045 .039 2.583 54 231 .042 .69 80 1900 5850 73 81 74 82 0 225 36 189 .035 179 142 28.895 .023 -4.853 -5.421 -4.853
3 413 163 101 54 312 109 394 131 106 58 293 77 0 0 172 129 29 25 100 68 96 53 421 370 2.862 .349 .263 .366 .419 4.3 32 146 .238 .35 60 2050 5840 73 79 90 96 0 110 36 73 .235 88 52 4.26 .177 -2.091 -2.502 -2.091
4 440 92 114 58 326 34 307 77 115 66 193 19 0 0 384 51 30 43 100 26 100 19 360 212 9.588 .104 .098 .157 .185 3.062 26 66 .027 .13 50 2200 5840 73 78 105 110 0 62 39 23 .07 52 13 14.269 .066 -3.835 -3.918 -3.835
5 238 86 106 55 132 31 212 79 110 56 106 24 0 0 111 48 28 15 97 61 85 33 163 130 4.258 .235 .226 .383 .404 3.33 42 178 .082 .18 70 2340 5850 73 80 118 125 0 58 37 21 .158 53 16 6.337 .152 -2.664 -2.717 -2.664
6 305 84 104 56 201 28 301 61 109 57 197 5 0 0 90 70 25 16 100 23 94 23 229 202 7.179 .139 .025 .103 .063 6.374 39 194 .1 .21 70 2490 5840 72 79 133 140 0 56 38 19 .094 41 3 10.683 .017 -3.417 -5.874 -3.417
7 246 68 107 57 139 11 224 59 112 60 117 2 0 0 69 25 34 20 100 29 85 11 150 119 12.636 .079 .017 .172 .236 3.007 34 150 .054 .19 60 2640 5840 73 79 149 155 0 46 38 7 .053 40 1 18.805 .011 -4.233 -6.444 -4.233
8 333 208 108 56 225 152 324 148 111 66 216 92 0 0 117 149 31 38 96 75 92 57 377 308 1.48 .676 .426 .434 .646 4.63 28 158 .81 .45 60 2780 5830 72 78 163 169 0 140 38 102 .454 99 62 2.203 .286 -1.139 -1.805 -1.139
9 414 361 101 52 313 309 318 236 104 59 217 184 0 0 321 349 30 30 88 91 84 74 622 401 1.013 .987 .848 .899 .812 6.681 59 246 1.168 .26 90 2920 5830 70 79 175 184 0 243 35 208 .663 159 124 1.507 .57 -.592 -.812 -.592
10 413 95 103 55 310 40 376 65 108 64 273 10 0 0 196 105 50 49 97 14 90 9 350 283 7.75 .129 .037 .087 .076 4.44 74 301 .097 .23 110 3070 5840 70 81 189 200 0 64 37 27 .087 44 7 11.533 .025 -3.528 -5.344 -3.528
11 1070 1712 104 56 966 1656 1000 1657 106 65 896 1601 0 0 584 743 25 43 100 100 100 100 2622 2497 .583 1.714 1.787 1.901 1.691 2.066 77 289 1.758 .78 100 3210 5840 71 81 204 214 0 1150 38 1113 1.152 1113 1076 .868 1.201 .204 .264 .204
12 5658 16610 104 55 5554 16555 5694 18374 107 61 5590 18319 0 0 2744 7218 31 23 100 100 100 100 22109 23909 .335 2.981 3.277 3.135 3.038 1.549 77 230 3.011 .95 90 3350 5840 71 80 218 227 0 11161 37 11124 2.003 12347 12310 .499 2.202 1.002 1.139 1.002
13 735 1043 102 55 633 988 649 992 106 60 547 937 0 0 469 595 43 27 93 100 93 98 1621 1484 .641 1.561 1.713 1.707 1.723 2.847 72 303 1.647 .71 100 3510 5840 71 81 234 244 0 701 37 664 1.049 667 630 .953 1.151 .069 .203 .069
14 137 496 102 55 35 441 113 449 107 59 11 394 0 0 91 251 43 26 20 100 10 98 476 405 .079 12.6 35.818 16.924 16.178 5.14 82 326 18.582 .18 110 3650 5840 70 81 247 258 0 333 37 296 8.467 302 265 .118 24.068 3.082 4.589 3.082
15 197 431 99 54 98 377 142 431 106 58 43 377 0 0 187 218 36 22 53 98 37 98 475 420 .26 3.847 8.767 4.03 4.324 4.664 69 199 6.029 .22 90 3800 5840 71 80 263 272 0 290 36 253 2.585 290 253 .387 5.891 1.37 2.559 1.37
16 20815 16073 102 54 20713 16019 22540 16244 107 62 22438 16190 0 0 11073 8608 31 57 100 100 100 100 36732 38628 1.293 .773 .722 .787 .765 1.22 81 292 .77 .98 100 3940 5840 71 81 277 287 0 10800 36 10764 .52 10915 10879 1.924 .485 -.944 -1.044 -.944
17 1082 1266 100 55 982 1211 1145 1166 104 64 1045 1111 0 0 506 624 29 65 100 100 100 100 2193 2156 .811 1.233 1.063 1.322 1.275 2.016 71 212 1.301 .78 90 4090 5840 71 80 292 301 0 851 37 814 .829 784 747 1.207 .714 -.271 -.485 -.271
18 346 2391 103 53 243 2338 260 2125 106 56 157 2072 0 0 264 992 32 16 79 100 73 100 2581 2229 .104 9.621 13.197 15.983 12.892 3.451 73 207 10.747 .58 90 4230 5840 71 80 306 315 0 1607 36 1571 6.465 1428 1392 .155 8.868 2.693 3.149 2.693
19 932 1468 103 55 829 1413 778 1264 119 63 675 1209 0 0 560 825 107 37 100 100 92 100 2242 1884 .587 1.704 1.791 1.77 1.736 1.974 82 267 1.776 .8 100 4380 5840 71 81 321 331 0 986 37 949 1.145 849 812 .873 1.204 .196 .267 .196
20 1276 1764 102 53 1174 1711 1338 1861 117 56 1236 1808 0 0 670 855 100 16 97 100 94 100 2885 3044 .686 1.457 1.463 1.505 1.576 2.04 79 284 1.448 .89 100 4520 5840 71 81 335 345 0 1185 36 1150 .979 1251 1215 1.021 .983 -.03 -.025 -.03

Total number of rows: 41472

Table truncated, full table size 9032 Kbytes.




Supplementary data files not provided
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