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Sample GSM90765 Query DataSets for GSM90765
Status Public on Jan 06, 2006
Title HUMAN 4 [HSR (human female) vs. HSJ (human male)]
Sample type genomic
 
Channel 1
Source name Human female genomic DNA
Organism Homo sapiens
Characteristics Human female genomic DNA
Extracted molecule genomic DNA
Label Cy3
 
Channel 2
Source name Human male genomic DNA
Organism Homo sapiens
Characteristics Human male genomic DNA
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: Comparative genomics, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/38129.gif
Data processing VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Jan 05, 2006
Last update date Feb 23, 2012
Organization Stanford Microarray Database (SMD)
E-mail(s) array@genome.stanford.edu
Phone 650-498-6012
URL http://genome-www5.stanford.edu/
Department Stanford University, School of Medicine
Street address 300 Pasteur Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL1448
Series (2)
GSE3980 Lineage-specific gene duplication and loss in human and great ape evolution
GSE9028 Extended Primate aCGH

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
LOG_RAT2N_MEAN 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
VALUE 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

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 LOG_RAT2N_MEAN VALUE
1 512 448 156 164 356 284 510 417 152 167 354 253 0 0 147 143 37 50 100 100 100 90 640 607 1.254 .798 .715 .763 .794 1.738 32 165 .768 .78 60 2130 7500 67 73 58 64 0 560 205 355 .998 521 316 1.002 .894 -.004 -.162
2 1044 808 145 152 899 656 1071 840 149 166 926 688 0 0 276 189 41 61 100 100 100 100 1555 1614 1.37 .73 .743 .734 .706 1.37 32 172 .725 .93 70 2270 7500 66 73 71 78 0 1010 190 820 .912 1050 860 1.096 .929 -.132 -.106
3 251 245 152 162 99 83 167 180 152 165 15 18 0 0 207 173 42 55 37 35 22 27 182 33 1.193 .838 1.2 1.112 .89 3.353 80 393 .824 .77 100 2390 7490 64 74 82 92 -50 306 203 104 1.048 225 23 .954 1.5 .068 .585
4 472 490 145 159 327 331 499 520 148 166 354 361 0 0 182 222 38 54 96 87 93 78 658 715 .988 1.012 1.02 .992 1.075 1.994 32 156 1.102 .84 60 2580 7490 66 72 103 109 0 613 199 414 1.266 650 451 .79 1.275 .34 .351
5 1166 1001 147 165 1019 836 1217 1005 152 170 1070 840 0 0 369 329 52 65 100 100 100 100 1855 1910 1.219 .82 .785 .809 .773 1.416 52 243 .821 .93 80 2710 7500 66 74 115 123 0 1252 206 1045 1.026 1257 1050 .975 .982 .037 -.027
6 892 686 147 161 745 525 797 617 152 170 650 456 0 0 428 271 57 71 100 93 96 90 1270 1106 1.419 .705 .702 .635 .736 2.09 32 205 .657 .86 70 2840 7480 64 71 128 135 0 858 201 656 .881 772 570 1.135 .877 -.183 -.189
7 846 760 147 161 699 599 814 725 151 168 667 564 0 0 217 188 56 57 100 100 100 100 1298 1231 1.167 .857 .846 .86 .864 1.332 32 203 .814 .91 70 3010 7500 66 73 145 152 0 950 201 749 1.072 907 705 .933 1.057 .1 .08
8 916 741 142 152 774 589 964 799 153 162 822 647 0 0 336 265 64 56 100 93 96 93 1363 1469 1.314 .761 .787 .755 .823 1.598 32 139 .728 .89 60 3130 7480 65 71 158 164 0 927 190 736 .952 999 809 1.051 .984 -.072 -.023
9 863 689 147 163 716 526 879 665 149 166 732 502 0 0 190 151 40 53 100 100 100 100 1242 1234 1.361 .735 .686 .731 .722 1.347 80 345 .727 .91 100 3270 7490 64 74 170 180 0 862 204 658 .919 832 628 1.089 .858 -.122 -.222
10 382 343 146 155 236 188 389 335 148 162 243 180 0 0 104 92 37 56 96 92 92 77 424 423 1.255 .797 .741 .8 .818 2.087 80 297 .768 .74 100 3420 7490 64 74 185 195 0 429 194 235 .996 419 225 1.004 .926 -.006 -.111
11 797 638 147 148 650 490 780 623 157 156 633 475 0 0 162 138 94 58 100 100 100 98 1140 1108 1.327 .754 .75 .745 .772 1.414 80 350 .736 .88 110 3560 7490 63 74 198 209 0 798 185 613 .943 779 594 1.061 .938 -.085 -.092
12 619 529 147 149 472 380 608 530 159 156 461 381 0 0 140 136 99 54 100 100 98 98 852 842 1.242 .805 .826 .787 .861 1.573 80 311 .743 .78 100 3710 7490 64 74 214 224 0 661 186 475 1.007 663 476 .993 1.033 .01 .047
13 1052 906 142 161 910 745 1067 920 144 165 925 759 0 0 277 227 37 52 100 100 100 100 1655 1684 1.221 .819 .821 .817 .808 1.368 80 312 .802 .93 100 3850 7490 64 74 228 238 0 1133 201 932 1.024 1150 949 .977 1.026 .034 .037
14 1002 675 143 159 859 516 990 672 144 163 847 513 0 0 231 160 39 55 100 100 100 100 1375 1360 1.665 .601 .606 .591 .588 1.468 80 324 .608 .9 100 4000 7490 64 74 243 253 0 844 199 645 .751 840 641 1.331 .757 -.413 -.401
15 583 506 143 161 440 345 576 498 145 163 433 337 0 0 140 108 39 58 100 100 100 100 785 770 1.275 .784 .778 .786 .778 1.517 80 302 .776 .86 100 4150 7490 64 74 258 268 0 633 201 431 .98 623 421 1.02 .973 -.029 -.039
16 227 239 144 165 83 74 145 173 150 167 1 8 0 0 470 365 42 57 17 23 10 10 157 9 1.122 .892 8 .929 .828 4.298 80 350 .806 .93 100 4290 7480 63 73 272 282 -50 299 206 93 1.115 216 10 .897 10.003 .157 3.322
17 1447 1243 146 164 1301 1079 1472 1269 150 165 1326 1105 0 0 414 303 40 53 100 100 100 100 2380 2431 1.206 .829 .833 .84 .851 1.265 80 328 .818 .96 100 4440 7490 64 74 287 297 0 1554 205 1349 1.037 1587 1382 .964 1.042 .052 .059
18 154 192 148 171 6 21 143 166 149 177 -5 -5 0 0 61 91 39 58 15 18 7 7 27 -10 .286 3.5 null 1.454 1.264 2.956 80 319 1.969 .37 100 4580 7480 63 73 301 311 -50 240 214 26 4.376 208 -6 .228 null 2.13 null
19 3272 2377 153 178 3119 2199 3360 2414 156 185 3207 2236 0 0 1012 624 48 70 100 100 100 100 5318 5443 1.418 .705 .697 .713 .71 1.209 80 309 .692 .97 100 4730 7490 64 74 316 326 0 2972 223 2750 .882 3018 2796 1.134 .872 -.182 -.198
20 809 640 147 172 662 468 800 621 150 179 653 449 0 0 195 141 48 67 100 100 100 100 1130 1102 1.415 .707 .688 .708 .712 1.413 80 308 .707 .89 100 4880 7490 64 74 331 341 0 800 215 585 .884 777 561 1.131 .86 -.178 -.218

Total number of rows: 43104

Table truncated, full table size 9798 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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