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Sample GSM741259 Query DataSets for GSM741259
Status Public on Nov 02, 2012
Title shfc77|NCIH747
Sample type genomic
 
Channel 1
Source name Normal human genomic DNA
Organism Homo sapiens
Characteristics reference: Normal human genomic DNA
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name NCIH747 genomic DNA
Organism Homo sapiens
Characteristics cell type: colorectal cancer
cell line: NCIH747
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol model: GenePix 4000B
Description Image: http://smd.stanford.edu/MicroArray/gifs/2006-07/69149.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 Jun 14, 2011
Last update date Nov 02, 2012
Contact name Keyan Salari
E-mail(s) [email protected]
Organization name Massachusetts General Hospital
Street address Gray/Bigelow Rm 1102, 55 Fruit Street
City Boston
State/province MA
ZIP/Postal code 02114
Country USA
 
Platform ID GPL9073
Series (2)
GSE29953 Colorectal Cancer Cell Lines aCGH
GSE30475 Colorectal Cancer Cells

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 3182 3728 316 598 2866 3130 3116 3675 341 691 2800 3077 0 0 538 1095 156 457 100 100 100 99 5996 5877 .916 1.092 1.099 1.1 1.05 .4 69 379 1.19 .99 90 2750 5330 64 73 82 91 0 3414 548 2867 1 3366 2818 1 1.006 0 .009
2 3825 4205 344 703 3481 3502 3716 4178 371 743 3372 3475 0 0 923 1266 173 459 100 100 100 98 6983 6847 .994 1.006 1.031 1.03 1.04 .37 52 331 1.12 .99 80 2900 5330 65 73 98 106 0 3851 644 3207 .921 3826 3183 1.085 .944 -.118 -.083
3 6364 8717 353 637 6011 8080 6031 8843 372 710 5678 8206 0 0 1534 2473 172 452 100 100 100 100 14091 13884 .744 1.344 1.445 1.36 1.32 .38 60 342 1.38 .99 80 3040 5330 65 73 112 120 0 7984 583 7400 1.231 8099 7516 .812 1.324 .3 .405
4 2609 4242 340 670 2269 3572 2525 4056 347 731 2185 3386 0 0 910 1785 163 449 100 100 100 98 5841 5571 .635 1.574 1.55 1.62 1.52 .67 52 359 1.65 .98 80 3190 5330 65 73 127 135 0 3885 614 3271 1.442 3715 3101 .694 1.419 .528 .505
5 2195 1634 328 651 1867 983 2124 1596 347 701 1796 945 0 0 488 631 165 422 100 83 100 56 2850 2741 1.899 .527 .526 .6 .56 .42 52 354 .76 .95 80 3340 5330 65 73 142 150 0 1497 596 900 .482 1462 865 2.074 .482 -1.052 -1.053
6 5470 7759 341 656 5129 7103 5643 7561 358 721 5302 6905 0 0 952 2048 168 432 100 100 100 100 12232 12207 .722 1.385 1.302 1.38 1.37 .34 44 374 1.42 .99 70 3480 5330 65 72 156 163 0 7106 601 6505 1.268 6925 6324 .788 1.193 .343 .254
7 1672 1414 328 639 1344 775 1559 1297 354 707 1231 658 0 0 736 762 174 430 100 64 98 39 2119 1889 1.734 .577 .535 .77 .52 .59 44 362 .88 .93 70 3630 5330 65 72 171 178 0 1295 585 710 .528 1188 603 1.894 .49 -.921 -1.03
8 4210 3530 315 667 3895 2863 4150 3618 344 733 3835 2951 0 0 1322 1188 165 438 100 100 99 97 6758 6786 1.36 .735 .769 .83 .72 .73 69 326 .85 .98 90 3770 5320 63 72 184 193 0 3233 611 2622 .673 3314 2703 1.485 .705 -.571 -.505
9 3159 3979 341 765 2818 3214 3176 3922 359 822 2835 3157 0 0 520 1154 173 495 100 100 100 98 6032 5992 .877 1.141 1.114 1.17 1.16 .5 86 280 1.26 .98 100 3910 5330 64 74 198 208 0 3644 701 2944 1.045 3592 2891 .957 1.02 .063 .028
10 5650 7370 339 705 5311 6665 5652 7587 359 776 5313 6882 0 0 936 1821 161 495 100 100 100 100 11976 12195 .797 1.255 1.295 1.26 1.28 .35 80 263 1.31 .99 100 4070 5330 64 74 214 224 0 6750 646 6104 1.149 6949 6303 .87 1.186 .201 .247
11 2674 2385 369 695 2305 1690 2608 2305 380 791 2239 1610 0 0 576 771 155 468 100 95 100 82 3995 3849 1.364 .733 .719 .76 .71 .41 80 275 .9 .97 100 4210 5330 64 74 228 238 0 2184 637 1548 .672 2111 1475 1.489 .659 -.575 -.603
12 3354 3794 383 703 2971 3091 3410 3713 380 799 3027 3010 0 0 579 942 162 452 100 100 100 100 6062 6037 .961 1.04 .994 1.07 1.02 .4 80 290 1.14 .99 100 4360 5330 64 74 243 253 0 3475 644 2831 .953 3401 2757 1.049 .911 -.07 -.135
13 3669 5187 355 691 3314 4496 3666 5150 373 790 3311 4459 0 0 740 1280 184 475 100 100 100 100 7810 7770 .737 1.357 1.347 1.39 1.33 .42 70 298 1.44 .99 90 4500 5330 64 73 257 266 0 4751 633 4118 1.243 4717 4084 .805 1.233 .313 .303
14 4300 4177 361 687 3939 3490 4275 3931 382 784 3914 3244 0 0 630 1257 189 470 100 100 100 100 7429 7158 1.129 .886 .829 .89 .84 .34 80 278 .97 .98 100 4650 5330 64 74 272 282 0 3826 629 3196 .811 3600 2971 1.232 .759 -.301 -.398
15 2004 2768 361 687 1643 2081 2043 2715 392 796 1682 2028 0 0 442 789 192 445 100 99 100 93 3724 3710 .79 1.267 1.206 1.34 1.32 .64 86 261 1.4 .98 100 4790 5330 64 74 286 296 0 2535 629 1906 1.16 2487 1857 .862 1.104 .214 .143
16 13075 14471 376 713 12699 13758 13536 14678 419 793 13160 13965 0 0 2382 3126 213 427 100 100 100 100 26457 27125 .923 1.083 1.061 1.08 1.06 .18 80 273 1.12 1 100 4940 5330 64 74 301 311 0 13253 653 12600 .992 13443 12790 1.008 .972 -.011 -.041
17 3833 5010 352 723 3481 4287 3820 5005 397 755 3468 4282 0 0 865 1461 206 432 100 99 100 99 7768 7750 .812 1.232 1.235 1.25 1.16 .48 80 260 1.32 .99 100 5090 5330 64 74 316 326 0 4588 662 3926 1.128 4584 3922 .887 1.131 .174 .177
18 5050 6227 353 726 4697 5501 5042 6217 386 814 4689 5491 0 0 850 1420 188 490 100 100 100 100 10198 10180 .854 1.171 1.171 1.19 1.14 .34 86 250 1.24 .99 100 5230 5330 64 74 330 340 0 5703 665 5038 1.073 5694 5029 .932 1.073 .101 .101
19 11708 15260 347 759 11361 14501 11637 15246 380 818 11290 14487 0 0 1949 2365 187 493 100 100 100 100 25862 25777 .783 1.276 1.283 1.29 1.28 .23 86 252 1.31 .99 100 5370 5330 64 74 344 354 0 13976 695 13281 1.169 13963 13268 .855 1.175 .225 .233
20 3100 2683 336 717 2764 1966 3144 2715 352 765 2808 1998 0 0 742 941 174 424 100 97 100 87 4730 4806 1.406 .711 .712 .74 .7 .35 97 282 .87 .97 110 5520 5320 62 73 358 369 0 2457 657 1801 .651 2487 1830 1.535 .652 -.618 -.618

Total number of rows: 41472

Table truncated, full table size 9733 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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