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Sample GSM90766 Query DataSets for GSM90766
Status Public on Jan 06, 2006
Title BONOBO 3 [HSE (human male) vs. BON5 (Bonobo male)]
Sample type genomic
 
Channel 1
Source name Human male genomic DNA
Organism Homo sapiens
Characteristics Human male genomic DNA
Extracted molecule genomic DNA
Label Cy3
 
Channel 2
Source name Bonobo male genomic DNA
Organism Homo sapiens
Characteristics Bonobo male genomic DNA
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: Comparative genomics, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40312.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 GPL3310
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
1 118 118 78 86 40 32 87 90 79 88 9 4 0 0 68 83 14 35 42 31 31 18 72 13 1.25 .8 .444 1.205 1.396 3.359 80 445 1.356 .6 100 2380 7210 52 62 89 99 -50 147 107 40 .998 112 5 1.002 .554 -.003 -.851
2 256 243 75 81 181 162 263 248 76 85 188 167 0 0 86 87 16 35 96 94 96 86 343 355 1.117 .895 .888 .936 .87 1.767 52 214 .966 .86 80 2540 7240 56 64 106 114 0 303 101 202 1.116 309 208 .896 1.108 .159 .148
3 85 99 75 86 10 13 75 92 76 90 0 6 0 0 52 45 14 35 17 22 5 11 23 6 .769 1.3 null 2.335 2.5 3.571 80 407 1.536 .31 100 2670 7210 52 62 118 128 -50 123 107 16 1.621 115 7 .617 null .697 null
4 192 136 77 81 115 55 179 136 77 86 102 55 0 0 76 63 15 33 93 59 84 46 170 157 2.091 .478 .539 .586 .653 1.924 32 165 .596 .53 60 2840 7220 55 61 137 143 0 170 101 69 .596 170 69 1.677 .672 -.746 -.573
5 394 320 77 83 317 237 382 324 77 87 305 241 0 0 124 118 15 34 96 93 96 90 554 546 1.338 .748 .79 .705 .732 1.774 32 223 .79 .9 70 2980 7230 55 62 150 157 0 399 104 296 .932 404 301 1.073 .985 -.101 -.021
6 270 247 77 90 193 157 267 247 80 93 190 157 0 0 66 59 20 38 100 100 96 87 350 347 1.229 .813 .826 .812 .763 1.737 32 165 .845 .82 60 3130 7230 56 62 166 172 0 308 112 196 1.014 308 196 .986 1.03 .021 .043
7 244 221 77 87 167 134 235 215 77 91 158 128 0 0 95 85 14 33 100 90 100 75 301 286 1.246 .802 .81 .784 .806 1.811 32 224 .895 .8 70 3280 7230 55 62 180 187 0 276 108 167 1.001 268 160 .999 1.01 .001 .015
8 244 220 76 85 168 135 230 191 77 93 154 106 0 0 78 91 15 35 100 93 100 75 303 260 1.244 .804 .688 .728 .807 2.587 32 152 .982 .78 60 3420 7230 56 62 195 201 0 274 106 168 1.002 238 132 .998 .858 .003 -.22
9 289 234 76 86 213 148 282 229 78 90 206 143 0 0 73 73 16 34 100 96 100 86 361 349 1.439 .695 .694 .612 .627 2.035 52 344 .715 .76 90 3540 7220 53 62 205 214 0 292 107 185 .867 286 178 1.154 .866 -.207 -.208
10 174 166 79 81 95 85 189 167 79 85 110 86 0 0 42 68 13 31 100 75 91 66 180 196 1.118 .895 .782 .696 .837 2.236 12 104 1.02 .71 50 3710 7210 54 59 224 229 0 207 101 106 1.116 208 107 .896 .975 .158 -.037
11 244 213 78 94 166 119 253 200 81 95 175 106 0 0 62 81 20 38 100 87 96 62 285 281 1.395 .717 .606 .542 .683 2.697 32 222 .924 .71 70 3840 7220 54 61 236 243 0 266 117 148 .894 249 132 1.119 .755 -.162 -.405
12 242 226 77 85 165 141 243 210 78 89 166 125 0 0 52 80 15 33 100 94 100 88 306 291 1.17 .855 .753 .743 .848 2.134 52 340 1.042 .78 90 3990 7220 53 62 250 259 0 282 106 176 1.066 262 156 .938 .939 .092 -.091
13 292 288 78 90 214 198 276 277 78 91 198 187 0 0 92 105 14 34 100 98 100 84 412 385 1.081 .925 .944 .847 .944 1.701 52 268 1.003 .86 90 4140 7220 53 62 265 274 0 359 112 247 1.154 345 233 .867 1.178 .206 .236
14 346 344 77 85 269 259 354 347 78 89 277 262 0 0 107 131 13 33 98 95 97 94 528 539 1.039 .963 .946 .922 .967 1.576 120 396 1.027 .91 120 4280 7220 52 64 278 290 0 429 106 323 1.201 433 327 .833 1.18 .264 .238
15 231 227 78 84 153 143 229 226 79 89 151 142 0 0 38 68 14 34 100 100 100 87 296 293 1.07 .935 .94 .858 .892 1.672 80 319 1.076 .77 110 4420 7220 52 63 292 303 0 283 105 178 1.166 282 177 .858 1.173 .221 .23
16 748 518 77 88 671 430 760 496 79 92 683 408 0 0 255 178 20 35 98 98 98 98 1101 1091 1.56 .641 .597 .646 .631 1.379 80 315 .623 .94 100 4560 7210 52 62 307 317 0 646 110 536 .799 619 509 1.251 .745 -.323 -.425
17 377 287 76 83 301 204 395 298 79 89 319 215 0 0 119 105 20 34 97 95 96 87 505 534 1.475 .678 .674 .643 .671 1.64 120 453 .711 .9 120 4720 7220 52 64 322 334 0 358 104 254 .845 372 268 1.183 .84 -.243 -.251
18 81 92 79 83 2 9 77 85 79 88 -2 2 0 0 20 41 13 33 16 22 5 5 11 0 .222 4.5 null 1.83 1.62 4.789 80 333 8.273 .18 100 4860 7210 52 62 337 347 -50 115 104 11 5.612 106 2 .178 null 2.488 null
19 708 611 79 83 629 528 655 556 80 90 576 473 0 0 289 254 13 37 100 100 100 100 1157 1049 1.191 .839 .821 .843 .845 1.324 52 265 .882 .94 90 5010 7220 53 62 352 361 0 762 104 658 1.047 693 590 .955 1.024 .066 .034
20 308 273 79 85 229 188 312 276 80 91 233 191 0 0 63 76 14 35 100 98 100 91 417 424 1.218 .821 .82 .773 .842 1.621 80 347 .861 .84 110 5150 7220 52 63 365 376 0 340 106 234 1.024 344 238 .977 1.022 .034 .032

Total number of rows: 43008

Table truncated, full table size 9196 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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