NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM40698 Query DataSets for GSM40698
Status Public on Jan 27, 2006
Title expression array - JPA3
Sample type RNA
 
Channel 1
Source name Cy3: Human Common Reference
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5: JPA3
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: tumor, Brain
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-10/56915
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 = 31.42; Parameter Scan Time = 20:28:40; Parameter PMT Volts = 560; Parameter Scan Date = 2004-10-05; Parameter Pixel Size = 10; Parameter Laser on time = 11116; 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 = 31.42; Parameter Scan Time = 20:28:40; Parameter PMT Volts = 660; Parameter Scan Date = 2004-10-05; Parameter Pixel Size = 10; Parameter Laser on time = 184721; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.54; 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) 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 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
1 345 144 83 51 262 93 347 95 93 64 264 44 0 0 107 113 52 104 97 34 92 21 355 308 2.817 .355 .167 .255 .319 5.061 41 154 .295 .31 70 1650 4980 58 65 33 40 0 96 34 62 .236 63 29 4.238 .111 -2.084 -3.174 -2.084
2 10616 1557 79 52 10537 1505 4564 751 88 62 4485 699 0 0 10945 1619 43 52 98 73 96 66 12042 5184 7.001 .143 .156 .121 .124 2.814 89 331 .134 .91 100 1800 4980 57 67 47 57 0 1035 35 1000 .095 499 465 10.534 .104 -3.397 -3.271 -3.397
3 899 423 78 54 821 369 817 338 92 65 739 284 0 0 685 377 59 50 94 73 94 63 1190 1023 2.225 .449 .384 .308 .404 3.234 38 168 .417 .72 70 1950 4980 58 65 63 70 0 281 36 245 .299 225 189 3.347 .255 -1.743 -1.969 -1.743
4 479 145 82 52 397 93 398 86 91 69 316 34 0 0 298 118 49 98 96 35 90 25 490 350 4.269 .234 .108 .199 .177 5.594 31 187 .142 .39 70 2090 4980 58 65 77 84 0 96 35 62 .156 57 23 6.422 .072 -2.683 -3.806 -2.683
5 352 139 78 53 274 86 235 66 80 71 157 13 0 0 310 153 20 97 100 25 95 17 360 170 3.186 .314 .083 .17 .2 6.669 40 172 .243 .39 70 2240 4970 57 64 92 99 0 92 35 57 .209 44 9 4.793 .055 -2.261 -4.183 -2.261
6 348 76 75 54 273 22 309 61 79 58 234 7 0 0 190 42 30 32 97 15 97 10 295 241 12.409 .081 .03 .068 .062 4.394 38 167 .061 .26 70 2390 4980 58 65 107 114 0 51 36 15 .054 41 5 18.67 .02 -4.223 -5.652 -4.223
7 351 122 77 51 274 71 261 77 81 56 184 26 0 0 238 84 29 36 96 45 93 33 345 210 3.859 .259 .141 .21 .217 4.93 33 187 .166 .48 70 2530 4980 58 65 121 128 0 81 34 47 .172 51 17 5.806 .094 -2.538 -3.412 -2.538
8 335 527 81 49 254 478 329 413 82 64 248 364 0 0 181 417 22 109 100 81 90 69 732 612 .531 1.882 1.468 1.524 2.105 2.88 33 180 2.714 .7 70 2680 4970 57 64 136 143 0 350 33 318 1.251 275 242 .799 .976 .323 -.036 .323
9 952 777 79 52 873 725 702 720 85 60 623 668 0 0 742 461 35 39 95 97 94 95 1598 1291 1.204 .83 1.072 .92 .853 3.988 73 242 .597 .6 90 2820 4970 56 65 149 158 0 516 35 482 .552 479 444 1.812 .713 -.857 -.489 -.857
10 664 163 78 53 586 110 552 120 89 66 474 67 0 0 432 155 65 85 97 42 90 22 696 541 5.327 .188 .141 .126 .173 5.994 70 300 .105 .34 100 2970 4970 56 66 164 174 0 108 35 73 .125 80 45 8.015 .094 -3.003 -3.412 -3.003
11 3220 4003 78 53 3142 3950 3516 4224 87 65 3438 4171 0 0 1472 2082 51 64 100 100 100 100 7092 7609 .795 1.257 1.213 1.202 1.222 1.805 76 298 1.339 .88 100 3120 4970 56 66 179 189 0 2661 35 2625 .836 2808 2772 1.197 .806 -.259 -.31 -.259
12 10943 41731 78 53 10865 41678 13481 55730 83 58 13403 55677 0 20 7081 26036 47 27 95 100 90 100 52543 69080 .261 3.836 4.154 5.278 3.965 3.221 96 340 3.86 .98 110 3270 4970 55 66 193 204 0 27737 35 27702 2.55 37042 37007 .392 2.761 1.35 1.465 1.35
13 1733 6103 79 53 1654 6050 1597 5946 88 57 1518 5893 0 0 923 2207 67 21 98 100 98 100 7704 7411 .273 3.658 3.882 4.329 3.741 2.313 70 218 3.898 .83 90 3410 4970 56 65 208 217 0 4056 35 4021 2.431 3952 3917 .411 2.58 1.282 1.368 1.282
14 248 451 77 53 171 398 134 367 134 144 57 314 0 0 248 343 819 1210 2 4 0 0 569 371 .43 2.327 5.509 3.585 3.947 7.175 73 290 308.546 .03 100 3550 4980 57 67 222 232 0 300 35 265 1.547 244 209 .646 3.662 .629 1.872 .629
15 275 4308 78 54 197 4254 169 4272 85 71 91 4218 0 0 254 1864 41 97 57 100 50 100 4451 4309 .046 21.594 46.352 45.56 30.263 5.002 75 210 24.84 .51 90 3700 4970 56 65 237 246 0 2863 36 2828 14.353 2839 2804 .07 30.809 3.843 4.945 3.843
16 41638 32859 80 54 41558 32805 61236 44300 88 66 61156 44246 33 0 27672 22605 50 84 100 100 100 100 74363 105402 1.267 .789 .723 .873 .805 1.873 95 345 .797 .98 110 3840 4970 55 66 250 261 0 21840 36 21805 .525 29445 29409 1.906 .481 -.93 -1.056 -.93
17 2700 8150 79 52 2621 8098 2727 7971 85 56 2648 7919 0 0 1107 3422 30 30 100 100 100 100 10719 10567 .324 3.09 2.991 3.119 3.088 1.862 73 205 3.513 .85 90 3990 4970 56 65 266 275 0 5417 35 5383 2.054 5298 5264 .487 1.988 1.038 .991 1.038
18 568 4573 78 53 490 4520 501 4498 85 59 423 4445 0 0 416 1891 34 32 88 100 84 100 5010 4868 .108 9.224 10.508 14.737 10.657 3.868 77 283 10.659 .66 100 4130 4970 56 66 280 290 0 3040 35 3004 6.131 2990 2954 .163 6.985 2.616 2.804 2.616
19 2507 1918 77 54 2430 1864 2403 1637 82 62 2326 1583 0 0 1164 1105 27 46 100 100 100 100 4294 3909 1.304 .767 .681 .707 .686 2.008 72 231 .777 .82 90 4280 4970 56 65 295 304 0 1275 36 1239 .51 1088 1052 1.961 .452 -.972 -1.144 -.972
20 2183 2948 77 53 2106 2895 2052 2805 84 62 1975 2752 0 0 1295 1532 38 44 98 100 97 100 5001 4727 .727 1.375 1.393 1.545 1.468 2.139 77 312 1.376 .85 100 4430 4970 56 66 310 320 0 1959 35 1924 .914 1864 1829 1.094 .926 -.13 -.111 -.13

Total number of rows: 41472

Table truncated, full table size 9204 Kbytes.




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