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Sample GSM874749 Query DataSets for GSM874749
Status Public on Dec 20, 2012
Title OV4004_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 OV4004
Organism Homo sapiens
Characteristics tissue: Primary tumor, Ovarian
age: 56 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): 5.07
progression-free survival (pfs, n=months): 4.9
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/2003-08/43882.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 GPL3528
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
1 435 374 182 151 253 223 434 355 190 167 252 204 0 0 74 84 48 68 100 100 100 91 476 456 1.135 .881 .81 .862 .864 1.353 12 90 .958 .79 50 1790 5580 43 48 52 57 0 356 144 212 .839 338 194 1.192 .771 -.253 -.376
2 440 440 175 165 265 275 445 429 176 167 270 264 0 0 98 90 36 47 100 100 100 100 540 534 .964 1.038 .978 1.062 1.037 1.473 12 98 1.061 .82 50 1930 5590 44 49 66 71 0 419 157 262 .988 408 251 1.012 .931 -.017 -.103
3 223 208 174 180 49 28 186 177 181 181 12 -3 0 0 121 114 42 49 36 23 23 11 77 9 1.75 .571 null 1.245 1.09 3.607 52 313 .981 .59 80 2080 5600 44 52 80 88 -50 198 171 27 .544 169 -3 1.838 null -.878 null
4 336 321 185 164 151 157 373 276 191 175 188 112 0 0 130 128 56 63 66 75 58 41 308 300 .962 1.04 .596 .766 1.082 2.05 12 98 1.135 .69 50 2230 5620 47 52 96 101 0 306 156 149 .99 263 107 1.01 .567 -.015 -.818
5 728 607 183 166 545 441 742 618 187 193 559 452 0 0 295 250 53 248 96 75 93 46 986 1011 1.236 .809 .809 .728 .774 1.797 32 160 .824 .94 60 2380 5590 44 50 111 117 0 578 158 420 .77 588 430 1.298 .77 -.376 -.377
6 353 312 181 169 172 143 369 317 194 176 188 148 0 0 77 42 62 56 91 100 83 75 315 336 1.203 .831 .787 .752 .717 1.576 12 90 .777 .73 50 2520 5580 43 48 125 130 0 297 161 136 .792 302 141 1.263 .75 -.337 -.416
7 249 226 186 168 63 58 226 206 190 169 40 38 0 0 95 99 41 42 48 46 25 25 121 78 1.086 .921 .95 1.22 1.165 3.746 52 300 1.188 .54 80 2660 5600 44 52 138 146 -50 215 160 55 .877 196 36 1.141 .905 -.19 -.145
8 591 578 184 176 407 402 595 522 188 180 411 346 0 0 132 174 36 45 100 100 100 100 809 757 1.012 .988 .842 .951 .929 1.31 12 98 1.063 .9 50 2810 5590 44 49 154 159 0 550 168 383 .94 497 329 1.063 .802 -.089 -.319
9 1152 1024 185 176 967 848 1211 1059 191 172 1026 883 0 0 249 240 40 37 100 100 100 100 1815 1909 1.14 .877 .861 .863 .892 1.382 32 160 .879 .95 60 2960 5590 44 50 169 175 0 975 168 807 .835 1008 841 1.198 .819 -.26 -.287
10 445 388 185 171 260 217 470 418 187 174 285 247 0 0 102 92 37 41 100 100 100 100 477 532 1.198 .835 .867 .821 .787 1.352 12 98 .714 .88 50 3100 5590 44 49 183 188 0 369 163 207 .795 398 235 1.258 .825 -.332 -.277
11 1005 992 184 177 821 815 993 1004 191 184 809 827 0 0 217 172 41 48 100 100 100 100 1636 1636 1.007 .993 1.022 1.021 .984 1.355 32 230 .96 .95 70 3250 5590 43 50 197 204 0 945 169 776 .945 956 787 1.058 .973 -.081 -.039
12 919 973 186 177 733 796 882 975 188 186 696 798 0 0 140 89 39 52 100 100 100 100 1529 1494 .921 1.086 1.147 1.097 1.048 1.152 12 90 1.16 .94 50 3390 5580 43 48 212 217 0 926 169 758 1.034 928 760 .967 1.092 .048 .127
13 747 835 190 166 557 669 711 826 200 174 521 660 0 0 148 109 61 67 100 100 100 100 1226 1181 .833 1.201 1.267 1.223 1.23 1.222 12 80 1.173 .9 50 3540 5570 42 47 227 232 0 795 158 637 1.144 786 628 .874 1.206 .194 .27
14 547 703 193 167 354 536 556 692 193 171 363 525 0 0 150 233 40 42 100 100 96 100 890 888 .66 1.514 1.446 1.479 1.553 1.422 32 160 1.552 .92 60 3690 5590 44 50 242 248 0 669 159 510 1.442 659 500 .694 1.377 .528 .462
15 986 1200 192 170 794 1030 1063 1212 195 171 871 1042 0 0 291 310 43 40 100 100 96 100 1824 1913 .771 1.297 1.196 1.383 1.265 1.483 32 222 1.273 .95 70 3830 5590 43 50 255 262 0 1143 162 981 1.235 1154 992 .81 1.139 .305 .188
16 3402 2861 182 174 3220 2687 3547 2962 186 173 3365 2788 0 0 978 813 45 36 100 100 100 100 5907 6153 1.198 .834 .829 .838 .824 1.284 32 164 .832 .98 60 3980 5590 44 50 271 277 0 2724 166 2558 .795 2820 2655 1.259 .789 -.332 -.342
17 1141 1244 185 181 956 1063 1253 1342 205 195 1068 1161 0 0 522 501 144 127 84 90 82 86 2019 2229 .899 1.112 1.087 1.211 1.122 1.506 52 268 1.099 .95 80 4120 5590 43 51 284 292 -100 1184 172 1012 1.059 1278 1105 .945 1.035 .082 .05
18 202 186 188 173 14 13 189 170 205 186 1 -3 0 0 71 61 138 125 5 5 1 0 27 -2 1.077 .929 null .706 .605 5.218 52 295 .929 .4 80 4270 5590 43 51 299 307 -50 177 165 12 .884 162 -3 1.131 null -.178 null
19 2526 2647 184 186 2342 2461 3023 2943 190 189 2839 2757 0 0 1091 1030 40 51 100 100 100 100 4803 5596 .952 1.051 .971 1.104 1.032 1.707 32 170 1.018 .97 60 4420 5600 45 51 315 321 0 2520 177 2343 1.001 2802 2625 .999 .925 .001 -.113
20 1439 1254 189 174 1250 1080 1419 1242 194 183 1230 1068 0 0 228 211 56 63 100 100 100 100 2330 2298 1.157 .864 .868 .862 .888 1.199 80 444 .861 .97 100 4580 5590 42 52 329 339 0 1194 166 1028 .823 1183 1017 1.216 .827 -.282 -.274

Total number of rows: 43104

Table truncated, full table size 9838 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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