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Sample GSM874857 Query DataSets for GSM874857
Status Public on Dec 20, 2012
Title OV3709_CGH
Sample type genomic
 
Channel 1
Source name universal reference
Organism Homo sapiens
Characteristics reference: universal reference
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name OV3709
Organism Homo sapiens
Characteristics tissue: Primary tumor, Ovarian
age: 57 years
tumor histology: serous
grade of tumor: 3
event (alive=1, dead=2): 2
progression (no progression=1, progression=2): 2
overall survival (os, n=months): 9.47
progression-free survival (pfs, n=months): 5.33
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol Scanner Model: GenePix 4000A
Description Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43460.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 Feb 13, 2012
Last update date Dec 20, 2012
Contact name Aslaug Helland
E-mail(s) aslaug.helland@medisin.uio.no
Phone +47-22934431
Organization name Institute for Cancer Research, Oslo University
Department Dept of Genetics
Street address Hospital Radiumhospitalet
City Oslo
ZIP/Postal code 0310
Country Norway
 
Platform ID GPL3522
Series (1)
GSE35783 CGH-arrays ovarian serous carcinomas.

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
1 169 247 143 259 26 -12 170 237 896 491 27 -22 0 0 52 71 5631 1669 0 0 0 0 14 5 null null null 1.435 1.545 2.403 52 296 .388 .92 80 1280 8610 53 61 32 40 -50 346 363 -17 null 332 -31 null null null null
2 302 428 137 216 165 212 289 438 1321 528 152 222 0 0 65 130 7384 1968 0 0 0 0 377 374 .778 1.285 1.461 1.115 1.191 2.37 32 164 1.705 .61 60 1440 8620 55 61 49 55 0 599 302 297 1.799 613 311 .556 2.045 .847 1.032
3 323 333 144 238 179 95 330 339 143 250 186 101 0 0 82 84 34 66 96 59 93 40 274 287 1.884 .531 .543 .533 .636 2.28 32 145 .841 .35 60 1600 8620 55 61 65 71 0 466 333 133 .743 475 141 1.345 .76 -.428 -.395
4 179 286 137 247 42 39 173 283 142 254 36 36 0 0 56 63 35 65 50 34 30 3 81 72 1.077 .929 1 .907 .911 2.998 52 270 10.018 .09 80 1720 8610 53 61 76 84 -50 401 346 55 1.3 396 50 .769 1.4 .379 .486
5 673 454 133 222 540 232 664 447 139 229 531 225 0 0 94 111 35 71 100 93 100 75 772 756 2.328 .43 .424 .376 .417 1.939 32 204 .464 .73 70 1890 8620 54 61 93 100 0 636 311 325 .602 626 315 1.662 .593 -.733 -.753
6 167 249 140 238 27 11 149 242 143 241 9 4 0 0 59 63 36 63 32 23 21 1 38 13 2.455 .407 .444 1.181 1.227 3.748 52 248 2.694 .26 80 2010 8610 53 61 105 113 -50 349 333 15 .571 339 6 1.753 .622 -.81 -.684
7 180 279 142 255 38 24 172 260 145 262 30 5 0 0 71 73 34 69 40 15 25 7 62 35 1.583 .632 .167 .751 .778 5.617 52 279 -1 -1 80 2150 8600 52 60 119 127 -50 391 357 34 .884 364 7 1.131 .233 -.177 -2.099
8 341 439 142 238 199 201 330 395 145 244 188 157 0 0 84 136 33 68 96 84 87 62 400 345 .99 1.01 .835 .987 1.142 2.184 32 151 1.494 .61 60 2320 8620 55 61 137 143 0 615 333 281 1.414 553 220 .707 1.169 .5 .226
9 563 487 140 242 423 245 549 481 151 246 409 239 0 0 124 127 123 75 100 92 92 80 668 648 1.727 .579 .584 .503 .53 2.053 52 294 .483 .69 90 2460 8610 52 61 149 158 0 682 339 343 .811 674 335 1.233 .818 -.302 -.289
10 185 237 146 236 39 1 177 224 159 248 31 -12 0 0 54 63 134 77 3 9 0 3 40 19 39 .026 null 1.58 1.444 4.282 52 244 3.39 .19 80 2590 8600 52 60 163 171 -50 332 330 1 .036 314 -17 27.849 null -4.8 null
11 334 358 142 233 192 125 323 346 146 239 181 113 0 0 70 76 36 63 100 76 100 44 317 294 1.536 .651 .624 .578 .596 1.961 52 345 .865 .58 90 2750 8610 52 61 178 187 0 501 326 175 .912 485 158 1.097 .874 -.133 -.194
12 351 390 143 246 208 144 341 408 147 254 198 162 0 0 81 98 35 69 100 75 96 57 352 360 1.444 .692 .818 .633 .708 2.303 52 268 .928 .64 80 2910 8610 53 61 195 203 0 546 344 202 .97 571 227 1.031 1.146 -.045 .196
13 243 324 150 244 93 80 239 314 151 253 89 70 0 0 44 71 39 67 87 53 62 15 173 159 1.163 .86 .787 .824 .847 2.839 32 144 2.768 .3 60 3040 8620 55 61 209 215 0 454 342 112 1.205 440 98 .83 1.101 .269 .139
14 291 321 143 232 148 89 284 302 195 235 141 70 0 0 58 93 597 61 0 53 0 26 237 211 1.663 .601 .496 .476 .536 2.861 52 287 .007 .03 90 3190 8610 52 61 222 231 0 450 325 125 .842 423 98 1.187 .695 -.248 -.524
15 363 380 141 246 222 134 347 391 186 249 206 145 0 0 86 93 534 65 0 76 0 58 356 351 1.657 .604 .704 .576 .616 2.236 80 359 .027 .12 110 3330 8620 52 63 235 246 0 532 344 188 .845 548 203 1.183 .986 -.242 -.021
16 2206 1663 138 241 2068 1422 2280 1682 144 253 2142 1441 0 0 678 578 35 79 100 98 100 98 3490 3583 1.454 .688 .673 .654 .659 1.282 52 278 .711 .95 90 3480 8610 52 61 251 260 0 2329 337 1991 .963 2355 2018 1.038 .942 -.054 -.086
17 355 384 143 251 212 133 350 377 146 259 207 126 0 0 72 82 34 78 100 75 97 36 345 333 1.594 .627 .609 .557 .654 2.361 80 357 .942 .56 110 3630 8610 51 62 265 276 0 538 352 186 .879 528 176 1.138 .852 -.187 -.23
18 150 243 146 260 4 -17 145 246 148 261 -1 -14 0 0 39 58 34 71 21 7 5 0 -13 -15 null null null 1.296 1 3.146 52 220 .141 .11 80 3760 8600 52 60 280 288 -50 340 364 -24 null 344 -20 null null null null
19 1290 1137 149 264 1141 873 1342 1219 250 358 1193 955 0 0 623 535 375 340 82 78 80 73 2014 2148 1.307 .765 .801 .807 .817 1.992 52 257 .906 .88 80 3900 8590 51 59 294 302 0 1592 370 1223 1.071 1707 1337 .933 1.121 .1 .165
20 332 365 146 248 186 117 326 354 201 299 180 106 0 0 63 85 276 258 11 6 0 0 303 286 1.59 .629 .589 .587 .609 2.171 80 397 .739 .89 110 4060 8610 51 62 308 319 0 511 347 164 .881 496 148 1.135 .825 -.183 -.278

Total number of rows: 43104

Table truncated, full table size 9458 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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