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Sample GSM741262 Query DataSets for GSM741262
Status Public on Nov 02, 2012
Title shgu239|SNUC2B
Sample type genomic
 
Channel 1
Source name Normal human female genomic DNA
Organism Homo sapiens
Characteristics reference: Norma human female genomic DNA
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name SNUC2B genomic DNA
Organism Homo sapiens
Characteristics cell type: colorectal cancer
cell line: SNUC2B
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/2006-08/69475.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 5994 4088 742 922 5252 3166 5981 4000 837 949 5239 3078 0 0 1209 1133 1000 498 99 99 99 99 8418 8317 1.659 .603 .588 .61 .57 .21 79 349 .7 .99 100 2620 5750 22 32 37 47 0 3132 706 2425 .462 3064 2358 2.166 .45 -1.115 -1.152
2 8222 7475 748 936 7474 6539 8042 7547 780 963 7294 6611 0 0 4573 2805 273 337 100 100 100 100 14013 13905 1.143 .875 .906 .93 .91 .28 54 272 .92 .99 80 2760 5760 24 32 52 60 0 5726 717 5009 .67 5781 5064 1.492 .694 -.577 -.526
3 8768 7498 756 892 8012 6606 8848 7768 785 935 8092 6876 0 0 1899 1766 282 460 100 100 100 100 14618 14968 1.213 .825 .85 .83 .82 .2 97 308 .86 .99 110 2900 5760 22 33 64 75 0 5744 683 5060 .632 5951 5267 1.583 .651 -.663 -.619
4 6826 7300 727 836 6099 6464 7064 7809 765 863 6337 6973 0 0 1980 2467 291 426 97 98 97 98 12563 13310 .944 1.06 1.1 1.14 1.05 .77 58 344 1.07 .99 80 3050 5770 25 33 81 89 0 5592 640 4952 .812 5982 5342 1.232 .843 -.301 -.247
5 5626 4198 717 829 4909 3369 5668 4119 750 828 4951 3290 0 0 1788 1156 298 286 100 100 100 100 8278 8241 1.457 .686 .665 .72 .74 .25 70 367 .76 .99 90 3200 5760 23 32 95 104 0 3216 635 2581 .526 3155 2520 1.902 .509 -.928 -.974
6 7179 7170 725 871 6454 6299 7094 6944 770 877 6369 6073 0 0 2148 2054 293 329 100 100 100 100 12753 12442 1.025 .976 .954 .98 .96 .18 34 372 1.01 .99 60 3350 5770 26 32 112 118 0 5493 667 4825 .748 5319 4652 1.338 .73 -.42 -.453
7 7174 6173 724 838 6450 5335 6916 6008 747 871 6192 5170 1 0 5403 3921 272 321 99 99 99 98 11785 11362 1.209 .827 .835 .94 .84 .71 151 246 .86 .98 140 3510 5760 21 35 124 138 0 4729 642 4087 .634 4602 3960 1.578 .64 -.658 -.645
8 6977 6184 717 841 6260 5343 6655 6046 735 877 5938 5205 0 0 3072 1304 265 306 100 100 100 100 11603 11143 1.172 .854 .877 .89 .89 .22 86 249 .9 .98 100 3640 5760 23 33 139 149 0 4737 644 4093 .654 4631 3987 1.529 .671 -.613 -.575
9 5111 5537 768 871 4343 4666 5077 5621 817 936 4309 4750 0 0 1109 992 383 445 100 100 100 100 9009 9059 .931 1.074 1.102 1.12 1.06 .33 80 307 1.09 .99 100 3790 5770 24 34 154 164 0 4242 667 3574 .823 4306 3639 1.215 .844 -.281 -.244
10 9146 8199 751 864 8395 7335 9054 8274 774 891 8303 7410 0 0 2577 2032 290 346 100 100 100 100 15730 15713 1.145 .874 .892 .88 .88 .16 51 332 .9 .99 80 3940 5760 24 32 170 178 0 6281 662 5619 .669 6338 5676 1.494 .684 -.579 -.549
11 3653 3908 728 845 2925 3063 3562 3744 765 903 2834 2899 0 0 883 829 299 370 100 100 100 100 5988 5733 .955 1.047 1.023 1.15 1.03 .55 86 360 1.07 .98 100 4080 5760 23 33 183 193 0 2994 647 2346 .802 2868 2221 1.247 .784 -.318 -.352
12 3830 4197 745 848 3085 3349 4288 4662 906 885 3543 3814 0 0 2188 2120 2824 333 62 86 12 81 6434 7357 .921 1.086 1.076 1.28 1.19 .51 42 335 1.11 .99 70 4240 5790 27 34 200 207 0 3215 650 2565 .832 3571 2922 1.203 .825 -.266 -.278
13 4628 5501 690 850 3938 4651 4409 5325 892 893 3719 4475 0 0 1416 1859 2871 445 87 100 9 100 8589 8194 .847 1.181 1.203 1.23 1.18 .41 97 327 1.19 .99 110 4370 5760 22 33 211 222 0 4214 651 3563 .905 4079 3428 1.105 .922 -.144 -.118
14 8151 7936 692 791 7459 7145 7610 7208 730 860 6918 6417 0 0 3471 5292 390 458 100 100 100 100 14604 13335 1.044 .958 .928 .95 .93 .44 80 267 .97 .98 100 4520 5770 24 34 227 237 0 6079 606 5473 .734 5522 4916 1.363 .711 -.447 -.493
15 3526 3985 642 780 2884 3205 2891 3545 733 872 2249 2765 1 0 5322 4409 853 655 99 100 83 97 6089 5014 .9 1.111 1.229 1.27 1.23 .55 151 211 1.15 .98 140 4660 5770 22 36 239 253 0 3053 598 2455 .851 2716 2118 1.175 .942 -.232 -.087
16 10421 13317 655 862 9766 12455 9982 13279 759 951 9327 12417 1 0 5648 3543 770 703 100 100 99 100 22221 21744 .784 1.275 1.331 1.4 1.35 .56 136 189 1.27 .98 130 4820 5780 23 36 255 268 0 10201 660 9541 .977 10172 9512 1.024 1.02 -.034 .028
17 6396 7484 684 843 5712 6641 4730 6208 723 846 4046 5365 0 0 7912 6884 256 279 100 100 100 100 12353 9411 .86 1.163 1.326 1.39 1.32 .53 80 240 1.19 .97 100 4960 5770 24 34 271 281 0 5733 646 5087 .891 4756 4110 1.123 1.016 -.167 .023
18 4944 6855 699 842 4245 6013 5007 6930 723 878 4308 6088 0 0 1622 1861 252 309 100 100 99 100 10258 10396 .706 1.416 1.413 1.51 1.45 .51 79 306 1.37 .98 100 5100 5760 23 33 285 295 0 5251 645 4606 1.085 5309 4664 .922 1.083 .118 .114
19 12412 15848 660 803 11752 15045 11367 15141 689 854 10707 14338 0 0 5182 3848 250 310 100 100 100 100 26797 25045 .781 1.28 1.339 1.34 1.33 .26 70 319 1.26 .99 90 5240 5770 24 33 299 308 0 12140 615 11525 .981 11599 10984 1.02 1.026 -.028 .037
20 5787 5751 650 785 5137 4966 4404 5829 683 836 3754 5044 0 0 6647 4429 241 302 90 88 86 86 10103 8798 1.034 .967 1.344 1.48 1.35 1.14 58 343 .99 .93 80 5400 5790 27 35 316 324 0 4406 601 3804 .741 4465 3864 1.35 1.029 -.433 .042

Total number of rows: 41472

Table truncated, full table size 9807 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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