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Sample GSM741243 Query DataSets for GSM741243
Status Public on Nov 02, 2012
Title shgu238|SW948
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 SW948 genomic DNA
Organism Homo sapiens
Characteristics cell type: colorectal cancer
cell line: SW948
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/2006-08/69476.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 4502 2882 555 771 3947 2111 4401 2802 597 804 3846 2031 0 0 919 706 284 335 100 100 100 100 6058 5877 1.87 .535 .528 .53 .53 .16 70 351 .65 .99 90 2560 6090 32 41 27 36 0 2269 607 1662 .421 2206 1599 2.374 .416 -1.248 -1.266
2 5387 6975 563 812 4824 6163 5561 6975 676 902 4998 6163 0 0 1628 2256 584 561 98 98 97 98 10987 11161 .783 1.278 1.233 1.3 1.3 .32 58 284 1.3 .99 80 2700 6100 34 42 42 50 0 5492 639 4853 1.006 5492 4853 .994 .971 .009 -.042
3 3814 3681 569 755 3245 2926 3134 2815 581 779 2565 2060 0 0 4497 4134 198 262 99 99 99 94 6171 4625 1.109 .902 .803 .98 .83 .68 86 286 .95 .98 100 2840 6100 33 43 55 65 0 2899 595 2304 .71 2217 1622 1.408 .632 -.494 -.661
4 5588 5735 599 767 4989 4968 5437 5978 605 791 4838 5211 0 0 2939 2596 200 253 97 93 93 93 9957 10049 1.004 .996 1.077 1.16 1.06 .99 60 361 1.03 .98 80 2990 6100 34 42 71 79 0 4516 604 3912 .784 4707 4103 1.275 .848 -.351 -.238
5 6738 4326 563 766 6175 3560 5842 3686 1030 883 5279 2920 0 0 5048 3504 4362 994 77 96 7 79 9735 8199 1.735 .577 .553 .56 .54 .23 70 351 .64 .97 90 3140 6100 33 42 85 94 0 3407 603 2803 .454 2903 2299 2.203 .436 -1.139 -1.199
6 7485 5222 567 780 6918 4442 5691 4008 1150 921 5124 3228 0 0 8676 5682 4663 1013 59 93 9 82 11360 8352 1.557 .642 .63 1.03 .67 2.13 44 356 .71 .98 70 3290 6110 35 42 101 108 0 4112 614 3498 .506 3156 2542 1.978 .496 -.984 -1.011
7 5462 3990 563 776 4899 3214 5475 3999 742 823 4912 3223 0 0 1085 979 2101 380 98 100 78 98 8113 8135 1.524 .656 .656 .65 .63 .19 133 248 .73 .99 130 3450 6090 30 43 114 127 0 3142 611 2531 .517 3149 2538 1.936 .517 -.953 -.953
8 5143 5632 574 791 4569 4841 5171 5739 627 814 4597 4948 0 0 1153 1259 296 309 100 100 100 100 9410 9545 .944 1.06 1.076 1.08 1.06 .27 104 211 1.1 .99 110 3580 6100 32 43 128 139 0 4435 623 3812 .834 4519 3896 1.199 .848 -.261 -.239
9 6631 5882 609 812 6022 5070 5055 5052 634 815 4446 4240 1 0 8893 4669 252 289 100 100 100 100 11092 8686 1.188 .842 .954 .98 1 .28 80 280 .89 .95 100 3730 6100 33 43 144 154 0 4632 639 3992 .663 3978 3339 1.508 .751 -.593 -.413
10 9789 6077 585 759 9204 5318 8721 5885 624 805 8136 5126 0 0 6157 1219 281 305 100 100 100 100 14522 13262 1.731 .578 .63 .64 .67 .15 44 298 .64 .97 70 3880 6100 34 41 160 167 0 4785 598 4188 .455 4634 4036 2.198 .496 -1.136 -1.011
11 6789 4828 584 776 6205 4052 3236 3291 652 826 2652 2515 1 0 10868 5446 383 424 94 97 94 96 10257 5167 1.531 .653 .948 1.2 .88 1.53 96 326 .76 .85 110 4010 6100 32 43 171 182 0 3802 611 3191 .514 2591 1980 1.945 .747 -.96 -.421
12 7722 10576 587 807 7135 9769 3953 4992 628 841 3366 4185 5 3 14239 15060 324 358 100 100 100 97 16904 7551 .73 1.369 1.243 1.66 1.14 1.91 37 370 1.4 .94 70 4180 6110 35 42 190 197 0 8328 635 7693 1.078 3931 3295 .928 .979 .109 -.031
13 4602 5641 583 733 4019 4908 3814 5472 616 778 3231 4739 0 0 4391 1474 213 260 100 100 100 100 8927 7970 .819 1.221 1.467 1.45 1.43 .47 86 302 1.22 .91 100 4310 6100 33 43 202 212 0 4442 577 3865 .962 4309 3732 1.04 1.155 -.056 .208
14 6024 4500 551 799 5473 3701 4902 3577 603 816 4351 2778 0 0 6242 5380 255 277 100 100 100 100 9174 7129 1.479 .676 .638 .65 .63 .22 86 238 .76 .93 100 4460 6100 33 43 217 227 0 3544 629 2914 .532 2817 2188 1.878 .503 -.909 -.992
15 3291 3544 582 833 2709 2711 3144 3549 657 876 2562 2716 0 0 1327 653 436 420 100 100 99 99 5420 5278 .999 1.001 1.06 1.09 1.03 .37 151 200 1.08 .96 140 4600 6100 31 45 229 243 0 2791 656 2135 .788 2795 2139 1.269 .835 -.344 -.261
16 10967 13739 565 764 10402 12975 11032 14012 586 788 10467 13248 0 0 3170 2798 200 290 100 100 100 100 23377 23715 .802 1.247 1.266 1.29 1.28 .29 136 180 1.25 .99 130 4760 6110 32 45 245 258 0 10819 602 10217 .982 11034 10432 1.018 .997 -.026 -.005
17 5343 6689 549 772 4794 5917 5276 6545 579 786 4727 5773 0 0 1479 1556 209 293 100 100 100 100 10711 10500 .81 1.234 1.221 1.25 1.28 .27 80 251 1.26 .99 100 4900 6100 33 43 261 271 0 5267 608 4659 .972 5154 4546 1.029 .962 -.041 -.056
18 5912 6472 558 756 5354 5716 4956 5507 650 787 4398 4751 0 0 6881 6454 1141 296 92 96 84 92 11070 9149 .937 1.068 1.08 1.14 1.05 .55 79 314 1.11 .97 100 5050 6090 32 42 276 286 0 5096 595 4501 .841 4336 3741 1.189 .851 -.25 -.233
19 11311 16991 545 752 10766 16239 11325 17676 653 788 10780 16924 0 0 3203 4144 1168 291 100 100 99 100 27005 27704 .663 1.508 1.57 1.54 1.54 .29 86 303 1.5 .99 100 5190 6100 33 43 290 300 0 13380 592 12787 1.188 13919 13327 .842 1.236 .248 .306
20 12587 12074 540 734 12047 11340 5893 5600 586 757 5353 4866 3 3 14408 15596 252 273 100 100 97 100 23387 10219 1.062 .941 .909 1.09 .94 1.09 36 351 .95 .97 70 5340 6120 36 43 306 313 0 9508 578 8930 .741 4410 3832 1.349 .716 -.432 -.482

Total number of rows: 41472

Table truncated, full table size 9687 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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