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Sample GSM741248 Query DataSets for GSM741248
Status Public on Nov 02, 2012
Title shgu237|SW1417
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 SW1417 genomic DNA
Organism Homo sapiens
Characteristics cell type: colorectal cancer
cell line: SW1417
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/2006-08/69477.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 5153 2721 654 714 4499 2007 5204 2738 703 773 4550 2024 0 0 787 632 423 457 100 100 100 97 6506 6574 2.242 .446 .445 .44 .44 .13 86 344 .54 .99 100 2630 5910 30 40 34 44 0 2410 632 1777 .395 2425 1792 2.531 .394 -1.34 -1.344
2 6463 5192 662 746 5801 4446 6627 5487 907 958 5965 4741 0 0 1662 1600 1044 983 100 97 93 89 10247 10706 1.305 .766 .795 .76 .74 .22 61 293 .81 .99 90 2770 5920 31 40 48 57 0 4598 661 3937 .679 4859 4198 1.473 .704 -.559 -.507
3 7862 6786 599 710 7263 6076 7927 7174 621 737 7328 6464 0 0 1817 1618 221 235 100 100 100 100 13339 13792 1.195 .837 .882 .84 .83 .19 97 291 .87 .99 110 2910 5920 30 41 61 72 0 6009 629 5381 .741 6353 5724 1.35 .781 -.433 -.356
4 6329 5211 595 721 5734 4490 6682 5424 625 738 6087 4703 0 0 1691 1625 227 241 100 100 100 98 10224 10790 1.277 .783 .773 .78 .8 .24 58 337 .83 .99 80 3060 5930 33 41 78 86 0 4615 638 3976 .693 4803 4165 1.442 .684 -.528 -.547
5 6062 3653 604 730 5458 2923 6246 3706 638 736 5642 2976 0 0 1465 984 242 234 99 99 99 99 8381 8618 1.867 .536 .527 .53 .53 .15 86 332 .61 .99 100 3210 5920 31 41 92 102 0 3235 646 2589 .474 3282 2635 2.109 .467 -1.076 -1.098
6 6058 4092 606 708 5452 3384 5966 4185 635 732 5360 3477 0 0 1550 934 251 239 100 100 100 97 8836 8837 1.611 .621 .649 .63 .65 .18 36 346 .68 .99 70 3360 5930 33 40 108 115 0 3624 627 2997 .55 3706 3079 1.819 .574 -.863 -.8
7 6053 4884 626 726 5427 4158 6179 5000 660 727 5553 4274 0 0 1428 1188 247 246 100 100 100 100 9585 9827 1.305 .766 .77 .78 .78 .21 140 237 .8 .99 130 3520 5920 29 42 121 134 0 4325 643 3682 .678 4428 3785 1.474 .682 -.56 -.553
8 5800 9161 574 717 5226 8444 5695 9368 615 722 5121 8651 0 0 1015 1339 244 261 100 100 100 100 13670 13772 .619 1.616 1.689 1.65 1.64 .35 86 243 1.57 .99 100 3650 5920 31 41 136 146 0 8113 635 7478 1.431 8296 7661 .699 1.496 .517 .581
9 5701 5689 563 717 5138 4972 5111 5787 585 736 4548 5070 0 0 4083 1378 212 244 100 100 100 100 10110 9618 1.033 .968 1.115 1.07 1.09 .29 86 293 1 .95 100 3800 5920 31 41 151 161 0 5038 635 4403 .857 5125 4490 1.167 .987 -.223 -.019
10 8111 5402 591 728 7520 4674 8405 5727 594 739 7814 4999 0 0 2891 1758 214 249 98 98 95 95 12194 12813 1.609 .622 .64 .69 .64 .44 60 299 .67 .99 80 3950 5920 32 40 167 175 0 4784 645 4139 .55 5072 4427 1.817 .567 -.861 -.82
11 3911 3568 603 768 3308 2800 3896 3573 613 798 3293 2805 0 0 937 706 240 295 100 100 100 100 6108 6098 1.181 .846 .852 .89 .87 .29 86 359 .91 .99 100 4080 5920 31 41 179 189 0 3160 680 2480 .75 3164 2484 1.334 .754 -.416 -.407
12 3967 4563 606 740 3361 3823 3708 4573 700 757 3102 3833 0 0 1021 1231 1592 271 97 100 44 100 7184 6935 .879 1.137 1.236 1.19 1.08 .47 34 350 1.14 .99 60 4240 5940 35 41 197 203 0 4041 655 3386 1.007 4050 3394 .993 1.094 .01 .13
13 4622 6060 612 727 4010 5333 4311 6018 723 741 3699 5291 0 0 1922 1441 1698 272 95 100 58 100 9343 8990 .752 1.33 1.43 1.45 1.39 .47 104 307 1.31 .98 110 4380 5920 30 41 208 219 0 5367 644 4723 1.178 5329 4686 .849 1.267 .236 .341
14 6667 7092 593 683 6074 6409 6681 7275 618 708 6088 6592 0 0 1265 1640 220 275 100 100 100 100 12483 12680 .948 1.055 1.083 1.04 1.04 .22 86 264 1.07 .99 100 4530 5920 31 41 224 234 0 6280 605 5676 .934 6443 5838 1.07 .959 -.098 -.061
15 3010 3626 569 677 2441 2949 3076 3588 613 706 2507 2911 0 0 717 739 258 270 99 100 99 99 5390 5418 .828 1.208 1.161 1.33 1.2 .75 166 178 1.2 .99 140 4670 5920 29 43 236 250 0 3211 600 2612 1.07 3177 2578 .935 1.028 .097 .04
16 11792 15137 570 668 11222 14469 12228 15591 614 673 11658 14923 0 0 3246 3485 267 249 99 100 99 100 25691 26581 .776 1.289 1.28 1.35 1.32 .39 124 198 1.28 .99 120 4820 5930 31 43 252 264 0 13405 592 12813 1.142 13807 13215 .876 1.134 .191 .181
17 5876 6451 568 639 5308 5812 5637 6522 596 664 5069 5883 0 0 1480 1242 220 225 100 100 100 100 11120 10952 .913 1.095 1.161 1.14 1.12 .35 80 246 1.1 .99 100 4960 5930 32 42 267 277 0 5713 566 5147 .97 5776 5210 1.031 1.028 -.044 .04
18 5976 6994 570 677 5406 6317 5942 7192 588 691 5372 6515 0 0 1805 1871 215 231 100 100 97 99 11723 11887 .856 1.169 1.213 1.21 1.22 .28 70 318 1.17 .99 90 5110 5920 31 40 282 291 0 6194 600 5594 1.035 6369 5769 .966 1.074 .049 .103
19 13858 18406 587 691 13271 17715 13887 18494 603 701 13300 17803 0 0 2630 3429 208 245 100 100 100 100 30986 31103 .749 1.335 1.339 1.34 1.33 .21 79 340 1.33 1 100 5250 5920 31 41 296 306 0 16300 612 15688 1.182 16378 15766 .846 1.185 .241 .245
20 5712 5339 569 664 5143 4675 5868 5377 591 686 5299 4713 0 0 1190 805 218 246 100 100 100 100 9818 10012 1.1 .909 .889 .94 .91 .23 37 405 .93 .99 70 5400 5930 33 40 312 319 0 4728 588 4140 .805 4762 4174 1.242 .788 -.313 -.344

Total number of rows: 41472

Table truncated, full table size 9695 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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