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Sample GSM741250 Query DataSets for GSM741250
Status Public on Nov 02, 2012
Title shgu233|COLO741
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 COLO741 genomic DNA
Organism Homo sapiens
Characteristics cell type: colorectal cancer
cell line: COLO741
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/2006-08/69651.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 4676 5250 537 591 4139 4659 4798 5213 574 625 4261 4622 0 0 641 869 379 299 100 100 100 100 8798 8883 .888 1.126 1.085 1.14 1.18 .25 86 336 1.11 .99 100 2680 6410 28 38 35 45 0 4697 529 4168 1.007 4664 4135 .993 .97 .01 -.043
2 6783 6190 520 586 6263 5604 7023 6347 740 721 6503 5761 0 0 1672 1579 1085 703 100 100 100 100 11867 12264 1.118 .895 .886 .91 .92 .22 61 299 .92 .99 90 2820 6420 29 38 49 58 0 5538 524 5014 .801 5679 5154 1.249 .793 -.321 -.335
3 4867 4799 488 565 4379 4234 5104 4860 510 594 4616 4295 0 0 1855 2060 281 288 99 100 99 98 8613 8911 1.034 .967 .93 1 .95 .53 97 298 .98 .99 110 2960 6420 28 39 62 73 0 4294 505 3788 .865 4348 3843 1.156 .832 -.209 -.265
4 5091 4941 500 605 4591 4336 5301 5139 519 620 4801 4534 0 0 1566 1610 217 265 100 98 98 97 8927 9335 1.059 .944 .944 .93 .93 .25 61 358 .97 .99 90 3110 6420 29 38 78 87 0 4421 541 3879 .845 4598 4056 1.183 .845 -.243 -.243
5 5133 4880 509 614 4624 4266 5143 4767 519 637 4634 4153 0 0 1186 1130 164 281 100 100 100 100 8890 8787 1.084 .923 .896 .94 .93 .24 80 319 .95 .99 100 3260 6420 29 39 93 103 0 4366 549 3817 .825 4265 3716 1.212 .802 -.277 -.319
6 2501 1696 512 614 1989 1082 2476 1608 536 640 1964 994 0 0 711 764 186 288 100 84 98 74 3071 2958 1.838 .544 .506 .61 .52 .42 61 317 .69 .96 90 3410 6420 29 38 108 117 0 1517 549 968 .487 1439 889 2.055 .453 -1.039 -1.143
7 5349 5196 499 576 4850 4620 5308 5131 555 609 4809 4555 0 0 1172 1277 312 319 100 99 100 99 9470 9364 1.05 .953 .947 .96 .95 .26 137 228 .97 .99 130 3560 6420 27 40 121 134 0 4649 515 4133 .852 4591 4075 1.173 .847 -.231 -.239
8 4777 4346 496 566 4281 3780 4707 4426 549 603 4211 3860 0 0 803 903 345 343 100 100 100 100 8061 8071 1.133 .883 .917 .9 .84 .26 86 244 .91 .99 100 3700 6420 29 39 137 147 0 3888 506 3382 .79 3960 3453 1.266 .82 -.34 -.286
9 5116 4729 529 575 4587 4154 5008 4870 554 616 4479 4295 0 0 931 1023 253 296 100 100 100 100 8741 8774 1.104 .906 .959 .9 .91 .19 86 269 .93 .99 100 3850 6420 29 39 152 162 0 4231 514 3716 .81 4357 3843 1.234 .858 -.304 -.221
10 9254 6954 509 596 8745 6358 9309 7207 537 632 8800 6611 0 0 1983 1767 245 292 100 100 100 100 15103 15411 1.375 .727 .751 .72 .74 .15 70 275 .75 .99 90 3990 6420 29 38 166 175 0 6222 533 5688 .65 6448 5915 1.537 .672 -.62 -.573
11 3777 4218 527 603 3250 3615 3723 4194 571 684 3196 3591 0 0 815 976 351 373 100 100 100 99 6865 6787 .899 1.112 1.124 1.14 1.15 .33 97 327 1.12 .99 110 4130 6410 27 38 179 190 0 3774 539 3234 .995 3752 3213 1.005 1.005 -.007 .008
12 2775 3163 520 606 2255 2557 3241 3432 539 634 2721 2826 0 0 1740 2000 207 283 80 80 75 75 4812 5547 .882 1.134 1.039 1.3 1.12 .84 80 282 1.14 .98 100 4280 6420 29 39 195 205 0 2830 542 2288 1.014 3071 2528 .986 .929 .021 -.106
13 6749 8324 523 591 6226 7733 6358 8176 543 633 5835 7585 0 0 1876 1882 191 280 100 100 100 100 13959 13420 .805 1.242 1.3 1.28 1.25 .29 97 297 1.23 .99 110 4420 6420 28 39 208 219 0 7447 529 6919 1.111 7315 6786 .9 1.163 .152 .218
14 6975 7548 533 592 6442 6956 6962 7504 543 631 6429 6912 0 0 1173 1372 187 285 100 100 100 100 13398 13341 .926 1.08 1.075 1.1 1.08 .28 86 256 1.09 .99 100 4570 6420 29 39 224 234 0 6753 530 6223 .966 6714 6184 1.035 .962 -.05 -.056
15 3427 4063 510 570 2917 3493 3431 4067 561 600 2921 3497 0 0 743 947 379 290 99 99 98 99 6410 6418 .835 1.197 1.197 1.26 1.19 .48 177 185 1.19 .99 150 4710 6420 26 41 235 250 0 3635 510 3125 1.071 3639 3129 .933 1.071 .099 .099
16 13717 16850 519 552 13198 16298 13864 16929 567 603 13345 16377 0 0 2438 2931 465 283 100 100 100 100 29496 29722 .81 1.235 1.227 1.24 1.27 .21 124 188 1.22 1 120 4870 6430 29 41 253 265 0 15075 494 14581 1.105 15146 14652 .905 1.098 .144 .135
17 7404 7512 523 612 6881 6900 7352 7519 539 678 6829 6907 0 0 1322 1239 178 286 100 100 100 100 13781 13736 .997 1.003 1.011 1.02 1 .22 86 241 1.02 .99 100 5010 6420 29 39 268 278 0 6721 548 6173 .897 6727 6180 1.115 .905 -.157 -.144
18 7605 8952 531 640 7074 8312 7966 9314 564 686 7435 8674 0 0 2142 2191 227 302 100 100 100 100 15386 16109 .851 1.175 1.167 1.26 1.16 .47 79 309 1.17 .99 100 5150 6410 28 38 282 292 0 8009 573 7437 1.051 8333 7760 .951 1.044 .072 .062
19 15007 22043 545 614 14462 21429 14347 22142 576 656 13802 21528 0 0 4435 4457 233 298 100 100 100 100 35891 35330 .675 1.482 1.56 1.52 1.54 .27 86 314 1.47 .99 100 5300 6420 29 39 297 307 0 19721 549 19172 1.326 19810 19261 .754 1.395 .407 .481
20 4901 6166 540 591 4361 5575 5059 6297 544 621 4519 5706 0 0 1033 1455 188 253 100 100 100 100 9936 10225 .782 1.278 1.263 1.29 1.3 .34 51 381 1.27 .99 80 5450 6420 30 38 313 321 0 5517 529 4988 1.144 5634 5105 .874 1.13 .194 .176

Total number of rows: 41472

Table truncated, full table size 9676 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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