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Sample GSM741256 Query DataSets for GSM741256
Status Public on Nov 02, 2012
Title SHGU225|COLO320
Sample type genomic
 
Channel 1
Source name Normal human female genomic DNA
Organism Homo sapiens
Characteristics reference: Normal human female genomic DNA
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name COLO320 genomic DNA
Organism Homo sapiens
Characteristics cell type: colorectal cancer
cell line: COLO320
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/2006-08/69937.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 GPL7780
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 5844 2392 725 868 5119 1524 5821 2353 758 916 5096 1485 0 0 861 549 323 359 100 98 100 93 6643 6581 3.359 .298 .291 .3 .29 .12 86 349 .42 .98 100 2620 5810 24 34 29 39 0 1989 722 1267 .248 1956 1235 4.04 .242 -2.014 -2.045
2 6586 3464 712 900 5874 2564 6848 3637 891 1071 6136 2737 0 0 1483 915 608 635 100 97 98 90 8438 8873 2.291 .436 .446 .43 .45 .14 58 313 .53 .99 80 2760 5820 26 34 44 52 0 2880 748 2132 .363 3024 2276 2.755 .371 -1.462 -1.431
3 7221 5942 702 850 6519 5092 7343 6000 744 873 6641 5150 0 0 1438 1298 284 261 100 100 100 100 11611 11791 1.28 .781 .775 .79 .78 .2 97 288 .83 .99 110 2900 5820 24 35 56 67 0 4940 707 4234 .649 4989 4282 1.54 .645 -.623 -.633
4 6190 3054 674 859 5516 2195 6420 3212 716 875 5746 2353 0 0 1575 796 268 265 98 100 97 97 7711 8099 2.513 .398 .41 .43 .41 .23 61 359 .51 .98 90 3050 5820 25 34 72 81 0 2539 714 1825 .331 2671 1956 3.022 .34 -1.596 -1.554
5 5403 2069 655 876 4748 1193 5398 2091 682 913 4743 1215 0 0 908 452 253 288 100 98 100 91 5941 5958 3.98 .251 .256 .25 .26 .1 80 323 .39 .99 100 3200 5820 25 35 87 97 0 1720 728 992 .209 1739 1010 4.787 .213 -2.259 -2.231
6 5784 3810 650 875 5134 2935 6275 3861 665 912 5625 2986 0 0 1335 873 234 291 98 100 98 96 8069 8611 1.749 .572 .531 1.48 .56 6.63 54 324 .67 .99 80 3350 5820 26 34 103 111 0 3168 728 2440 .475 3210 2483 2.104 .441 -1.073 -1.18
7 5355 3100 691 889 4664 2211 5421 3090 690 910 4730 2201 0 0 1014 617 215 275 100 100 100 100 6875 6931 2.109 .474 .465 .48 .47 .15 136 219 .59 .99 130 3500 5820 23 36 115 128 0 2577 739 1838 .394 2569 1830 2.537 .387 -1.343 -1.37
8 4321 3214 656 904 3665 2310 4243 3151 670 935 3587 2247 0 0 726 655 222 345 100 100 100 100 5975 5834 1.587 .63 .626 .65 .62 .23 97 232 .76 .98 110 3630 5820 24 35 129 140 0 2672 752 1921 .524 2620 1868 1.908 .521 -.932 -.941
9 3756 3833 625 934 3131 2899 3682 3856 665 954 3057 2922 0 0 806 657 240 310 100 100 100 100 6030 5979 1.08 .926 .956 .97 .95 .31 86 274 1.03 .98 100 3780 5820 25 35 145 155 0 3187 777 2410 .77 3206 2429 1.299 .795 -.377 -.331
10 6945 4934 657 924 6288 4010 7132 5090 675 941 6475 4166 0 0 1968 1169 238 248 100 99 100 97 10298 10641 1.568 .638 .643 .65 .63 .18 72 303 .72 .99 90 3930 5810 24 33 160 169 0 4102 768 3334 .53 4232 3464 1.886 .535 -.915 -.903
11 2796 3260 651 887 2145 2373 2844 3198 676 924 2193 2311 0 0 686 555 231 295 100 100 97 100 4518 4504 .904 1.106 1.054 1.26 1.04 .65 96 322 1.16 .99 110 4070 5820 24 35 173 184 0 2710 737 1973 .92 2659 1921 1.087 .876 -.121 -.191
12 4871 5031 642 865 4229 4166 4728 5161 665 900 4086 4296 0 0 1418 1155 230 277 100 100 100 100 8395 8382 1.015 .985 1.051 1.07 .98 .46 44 316 1.04 .99 70 4220 5840 28 35 190 197 0 4183 719 3464 .819 4291 3572 1.221 .874 -.288 -.194
13 3706 5628 668 867 3038 4761 3695 5731 678 893 3027 4864 0 0 924 1083 220 285 100 100 100 100 7799 7891 .638 1.567 1.607 1.7 1.59 .68 104 300 1.51 .98 110 4360 5820 24 35 202 213 0 4679 721 3958 1.303 4765 4044 .767 1.336 .382 .418
14 6904 4219 636 876 6268 3343 6889 4087 657 909 6253 3211 0 0 897 685 233 277 100 100 100 100 9611 9464 1.875 .533 .514 .53 .52 .13 86 259 .62 .99 100 4510 5820 25 35 218 228 0 3508 728 2779 .443 3398 2670 2.255 .427 -1.173 -1.228
15 2589 3146 603 917 1986 2229 2555 3170 627 943 1952 2253 0 0 564 612 233 273 99 100 99 99 4215 4205 .891 1.122 1.154 1.18 1.11 .48 156 167 1.23 .98 140 4650 5830 24 38 230 244 0 2616 762 1853 .933 2636 1873 1.072 .96 -.1 -.059
16 12846 14264 623 916 12223 13348 13203 14692 678 932 12580 13776 0 0 2535 2811 288 276 99 100 99 100 25571 26356 .916 1.092 1.095 1.16 1.09 .76 140 220 1.11 .99 130 4800 5820 23 36 245 258 0 11860 762 11098 .908 12215 11454 1.101 .91 -.139 -.135
17 4987 6323 638 863 4349 5460 5045 6203 664 901 4407 5340 0 0 1186 1320 247 275 100 100 100 100 9809 9747 .797 1.255 1.212 1.3 1.32 .32 86 252 1.27 .99 100 4950 5820 25 35 262 272 0 5257 718 4540 1.044 5157 4440 .958 1.007 .062 .011
18 5179 7591 630 907 4549 6684 4799 7919 875 962 4169 7012 1 0 6876 5259 2798 630 76 93 12 89 11233 11181 .681 1.469 1.682 1.65 1.61 .54 84 275 1.48 .94 110 5100 5810 23 34 276 287 0 6311 754 5557 1.222 6584 5830 .819 1.398 .289 .484
19 11407 17521 661 906 10746 16615 11379 18127 902 965 10718 17221 0 0 2466 3564 2771 619 100 100 98 100 27361 27939 .647 1.546 1.607 1.55 1.54 .25 80 280 1.54 .99 100 5240 5830 26 36 291 301 0 14567 753 13814 1.286 15071 14318 .778 1.336 .362 .418
20 3863 4757 630 879 3233 3878 4299 4812 649 902 3669 3933 0 0 1366 1500 225 271 100 98 97 98 7111 7602 .834 1.2 1.072 1.41 1.16 1.14 60 356 1.24 .99 80 5390 5830 27 35 307 315 0 3955 731 3224 .997 4001 3270 1.003 .891 -.004 -.166

Total number of rows: 41472

Table truncated, full table size 9813 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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