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Sample GSM229015 Query DataSets for GSM229015
Status Public on Feb 24, 2012
Title Expt. #8.4-Baboon2
Sample type genomic
 
Channel 1
Source name Reference
Organism Homo sapiens
Characteristics Reference
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name Test
Organism Papio hamadryas
Characteristics Test
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol not provided
Description Simple annotation: Comparative genomics, DNA
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 Sep 12, 2007
Last update date Feb 24, 2012
Organization Stanford Microarray Database (SMD)
E-mail(s) [email protected]
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 GPL5846
Series (1)
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
1 932 285 257 193 675 92 974 282 263 202 717 89 0 0 364 80 57 74 91 56 91 25 767 806 7.337 .136 .124 .55 .15 1.98 32 466 .33 .94 60 2060 6200 61 67 63 69 0 421 285 136 .201 416 131 4.97 .183 -2.313 -2.448
2 615 360 247 194 368 166 633 334 251 204 386 140 0 0 325 154 82 76 68 65 68 49 534 526 2.217 .451 .363 .73 .46 1.46 37 415 .59 .9 70 2210 6210 61 68 77 84 0 531 286 245 .666 493 207 1.502 .535 -.587 -.901
3 1180 535 235 195 945 340 1159 444 244 209 924 249 0 0 416 268 103 120 100 81 100 54 1285 1173 2.779 .36 .269 .33 .29 .18 26 436 .47 .97 50 2350 6200 61 66 92 97 0 790 288 502 .531 655 368 1.883 .398 -.913 -1.33
4 835 325 232 189 603 136 858 348 240 206 626 159 0 0 262 109 97 122 96 58 96 8 739 785 4.434 .226 .254 .31 .23 .39 26 444 .4 .91 50 2490 6190 60 65 106 111 0 480 279 201 .333 514 235 3.003 .375 -1.587 -1.415
5 633 309 231 184 402 125 633 310 235 193 402 126 0 0 162 102 53 79 100 62 96 46 527 528 3.216 .311 .313 .39 .33 .31 26 470 .51 .94 50 2630 6190 60 65 120 125 0 456 272 185 .459 458 186 2.178 .463 -1.123 -1.112
6 687 289 232 192 455 97 329 270 287 204 97 78 0 0 486 110 958 84 30 49 0 30 552 175 4.691 .213 .804 1.14 .21 2.85 37 473 .43 .92 70 2800 6190 59 66 136 143 -50 427 283 143 .315 399 115 3.177 1.187 -1.668 .247
7 612 373 228 202 384 171 545 339 297 222 317 137 0 0 395 192 1013 115 8 54 0 32 555 454 2.246 .445 .432 .92 .42 1.72 37 427 .64 .96 70 2940 6190 59 66 150 157 0 551 298 252 .657 500 202 1.521 .638 -.605 -.648
8 881 416 225 196 656 220 888 386 239 214 663 190 0 0 322 177 114 111 94 63 94 41 876 853 2.982 .335 .287 .36 .31 .25 32 396 .49 .96 60 3070 6200 61 67 164 170 0 614 289 325 .495 570 280 2.02 .423 -1.014 -1.241
9 466 332 227 194 239 138 456 330 241 209 229 136 0 0 89 106 226 101 53 67 0 25 377 365 1.732 .577 .594 .85 .64 1.14 36 430 .72 .95 70 3220 6200 60 67 178 185 0 490 286 204 .852 487 201 1.173 .877 -.23 -.19
10 868 477 228 203 640 274 937 468 249 214 709 265 0 0 244 199 240 101 89 81 72 58 914 974 2.336 .428 .374 .44 .43 .28 36 395 .57 .97 70 3380 6170 57 64 194 201 0 704 300 405 .632 691 391 1.582 .552 -.662 -.858
11 429 230 241 209 188 21 398 210 260 223 157 1 0 0 171 133 155 164 51 7 9 2 209 158 8.952 .112 .006 .69 .35 1.13 86 362 .53 .4 100 3510 6170 56 66 206 216 0 340 309 31 .165 310 1 6.064 .009 -2.6 -6.733
12 766 469 237 204 529 265 745 439 250 215 508 235 0 0 189 139 110 91 100 94 94 81 794 743 1.996 .501 .463 .52 .5 .25 32 417 .62 .98 60 3670 6170 58 64 224 230 0 692 301 391 .74 648 347 1.352 .683 -.435 -.55
13 319 252 231 207 88 45 297 244 235 209 66 37 0 0 118 69 51 71 54 38 46 11 133 103 1.956 .511 .561 1.16 .67 1.48 37 406 .79 .9 70 3820 6190 59 66 238 245 -50 372 306 66 .755 360 55 1.325 .828 -.406 -.273
14 997 495 228 206 769 289 1086 479 235 219 858 273 0 0 306 164 67 114 100 82 95 64 1058 1131 2.661 .376 .318 .5 .35 .65 44 413 .5 .95 70 3960 6180 58 65 252 259 0 731 304 427 .555 707 403 1.802 .47 -.85 -1.09
15 402 240 220 204 182 36 389 234 223 214 169 30 0 0 107 86 53 111 87 16 81 0 218 199 5.056 .198 .178 .65 .52 .6 31 460 .62 .62 60 4110 6170 58 64 268 274 0 354 301 53 .292 345 44 3.424 .262 -1.776 -1.932
16 1032 914 222 209 810 705 968 878 223 213 746 669 0 0 476 392 45 76 100 96 96 92 1515 1415 1.149 .87 .897 1.09 .81 .92 26 408 .9 .99 50 4260 6170 58 63 283 288 0 1349 309 1041 1.285 1296 988 .778 1.324 .362 .405
17 352 400 223 201 129 199 296 247 225 208 73 46 0 0 134 1013 47 82 60 33 48 15 328 119 .648 1.543 .63 1.57 .62 2.47 52 388 1 .26 80 4390 6180 58 66 295 303 0 591 297 294 2.277 365 68 .439 .93 1.187 -.104
18 475 354 221 206 254 148 453 353 227 216 232 147 0 0 114 102 72 86 100 70 84 38 402 379 1.716 .583 .634 .75 .48 .73 37 457 .75 .96 70 4540 6170 57 64 310 317 0 523 304 218 .86 521 217 1.163 .935 -.217 -.096
19 1551 1190 217 210 1334 980 1528 1123 227 220 1311 913 0 0 496 433 81 82 100 100 98 100 2314 2224 1.361 .735 .696 .78 .75 .34 44 405 .76 .99 70 4690 6170 57 64 325 332 0 1757 310 1447 1.085 1658 1348 .922 1.028 .117 .04
20 531 417 215 211 316 206 510 420 222 219 295 209 0 0 110 100 76 76 100 89 95 68 522 504 1.534 .652 .708 .71 .64 .39 44 417 .79 .97 70 4830 6180 58 65 339 346 0 616 312 304 .962 620 309 1.039 1.046 -.055 .065

Total number of rows: 43008

Table truncated, full table size 9318 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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