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Sample GSM741245 Query DataSets for GSM741245
Status Public on Nov 02, 2012
Title shgu227|LIM2412
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 LIM2412 genomic DNA
Organism Homo sapiens
Characteristics cell type: colorectal cancer
cell line: LIM2412
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/2006-08/69843.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 5467 3480 702 944 4765 2536 5424 3467 744 1000 4722 2523 0 0 920 842 387 578 100 100 100 97 7301 7245 1.879 .532 .534 .54 .53 .19 86 310 .65 .98 100 2630 5790 30 40 30 40 0 2712 736 1977 .415 2702 1967 2.411 .416 -1.269 -1.264
2 6999 6293 718 957 6281 5336 7482 6452 848 1113 6764 5495 0 0 1826 1580 769 973 100 98 95 97 11617 12259 1.177 .85 .812 .99 .82 .73 61 272 .91 .99 90 2770 5800 31 40 44 53 0 4905 746 4159 .662 5029 4283 1.51 .633 -.595 -.659
3 8976 9298 679 932 8297 8366 8802 9143 835 978 8123 8211 0 0 1724 1857 1976 503 100 100 100 100 16663 16334 .992 1.008 1.011 1.01 1 .19 80 297 1.03 .99 100 2920 5800 31 41 59 69 0 7247 726 6521 .786 7126 6400 1.272 .788 -.348 -.344
4 6831 7130 692 992 6139 6138 6873 7563 815 987 6181 6571 0 0 2149 2204 1831 386 95 100 89 97 12277 12752 1 1 1.063 1.18 1.04 1 61 334 1.06 .99 90 3060 5800 31 40 73 82 0 5557 773 4784 .779 5895 5122 1.283 .829 -.36 -.271
5 7445 6593 679 984 6766 5609 7261 6541 698 1014 6582 5557 0 0 1659 1598 242 376 100 100 100 100 12375 12139 1.206 .829 .844 .83 .81 .19 70 349 .89 .99 90 3210 5800 31 40 88 97 0 5139 767 4372 .646 5098 4331 1.548 .658 -.63 -.604
6 5969 5828 678 960 5291 4868 5869 5778 750 990 5191 4818 0 0 2177 2068 970 348 97 100 93 100 10159 10009 1.087 .92 .928 1.16 .9 1.3 58 292 .98 .98 80 3360 5810 33 41 104 112 0 4543 748 3794 .717 4504 3755 1.394 .723 -.48 -.467
7 5258 4242 723 944 4535 3298 5005 3999 814 991 4282 3055 0 0 2400 2071 1168 366 98 98 78 94 7833 7337 1.375 .727 .713 .74 .69 .32 124 196 .81 .98 120 3510 5800 30 42 117 129 0 3306 736 2571 .567 3117 2381 1.764 .556 -.819 -.847
8 6020 6682 698 930 5322 5752 5961 6583 746 1010 5263 5653 0 0 1244 1345 317 589 100 100 100 100 11074 10916 .925 1.081 1.074 1.11 1.08 .29 97 223 1.11 .99 110 3640 5800 30 41 130 141 0 5208 725 4483 .842 5131 4406 1.187 .837 -.247 -.256
9 5590 6166 674 931 4916 5235 5661 6165 710 1019 4987 5234 0 0 1127 1072 293 543 100 100 100 100 10151 10221 .939 1.065 1.05 1.1 1.08 .31 86 256 1.11 .99 100 3800 5800 31 41 147 157 0 4806 726 4080 .83 4805 4080 1.205 .818 -.269 -.29
10 10352 8454 657 925 9695 7529 10280 8064 681 977 9623 7139 0 0 2626 1890 253 355 100 100 100 100 17224 16762 1.288 .777 .742 .79 .79 .16 58 287 .82 .99 80 3940 5800 32 40 162 170 0 6589 721 5868 .605 6285 5564 1.652 .578 -.724 -.79
11 3745 6226 686 934 3059 5292 3758 6209 696 1001 3072 5275 0 0 1087 1220 263 396 99 100 99 100 8351 8347 .578 1.73 1.717 1.93 1.79 .87 104 316 1.65 .99 110 4080 5800 30 41 174 185 0 4853 728 4125 1.348 4840 4112 .742 1.338 .431 .421
12 4924 5851 708 908 4216 4943 5095 5637 716 956 4387 4729 0 0 1864 2266 275 373 96 98 94 98 9159 9116 .853 1.172 1.078 1.35 1.14 1.08 52 298 1.19 .98 80 4240 5820 34 42 192 200 0 4561 708 3853 .914 4394 3686 1.094 .84 -.13 -.251
13 4820 6034 684 978 4136 5056 4394 5866 704 1009 3710 4888 0 0 1714 1466 260 376 100 100 100 100 9192 8598 .818 1.222 1.318 1.3 1.28 .39 97 274 1.25 .98 110 4370 5800 30 41 203 214 0 4703 762 3941 .953 4572 3810 1.05 1.027 -.07 .038
14 8400 7011 686 978 7714 6033 8459 7043 710 1016 7773 6065 0 0 1375 1229 258 391 100 100 100 100 13747 13838 1.279 .782 .78 .78 .79 .16 86 228 .83 .99 100 4520 5800 31 41 219 229 0 5465 762 4702 .61 5490 4727 1.64 .608 -.714 -.717
15 3330 4352 643 933 2687 3419 3289 4301 678 973 2646 3368 0 0 742 887 253 360 100 100 100 100 6106 6014 .786 1.272 1.273 1.35 1.27 .49 166 179 1.3 .99 140 4660 5810 30 44 231 245 0 3392 727 2665 .992 3352 2625 1.008 .992 -.012 -.011
16 11999 18512 697 927 11302 17585 11912 18626 704 964 11215 17699 0 0 3052 4433 263 335 100 100 100 100 28887 28914 .643 1.556 1.578 1.58 1.59 .28 136 188 1.54 .99 130 4820 5810 30 43 247 260 0 14429 723 13707 1.213 14518 13795 .825 1.23 .278 .299
17 7041 11442 683 961 6358 10481 6908 11521 693 996 6225 10560 0 0 1858 2303 258 338 100 100 100 100 16839 16785 .607 1.648 1.696 1.73 1.69 .43 86 225 1.62 .99 100 4960 5800 31 41 263 273 0 8918 749 8169 1.285 8980 8231 .778 1.322 .362 .403
18 6161 8118 697 966 5464 7152 6349 8363 726 1015 5652 7397 0 0 2009 2330 258 366 99 97 97 97 12616 13049 .764 1.309 1.309 1.33 1.32 .39 79 267 1.31 .99 100 5110 5800 31 41 278 288 0 6328 753 5575 1.02 6519 5766 .98 1.02 .029 .029
19 17946 22872 708 965 17238 21907 18300 23191 730 1018 17592 22226 0 0 3850 4279 253 392 100 100 100 100 39145 39818 .787 1.271 1.263 1.29 1.25 .24 79 292 1.28 .99 100 5250 5800 31 41 292 302 0 17827 752 17075 .991 18076 17324 1.01 .985 -.014 -.022
20 6451 7703 669 954 5782 6749 6356 7426 702 981 5687 6472 0 0 2011 1786 296 354 100 100 100 100 12531 12159 .857 1.167 1.138 1.27 1.14 .54 44 374 1.18 .99 70 5400 5820 34 41 308 315 0 6004 744 5260 .91 5788 5045 1.099 .887 -.136 -.173

Total number of rows: 41472

Table truncated, full table size 9795 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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