NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM741269 Query DataSets for GSM741269
Status Public on Nov 02, 2012
Title SHGU226|LS411
Sample type genomic
 
Channel 1
Source name Normal human male genomic DNA
Organism Homo sapiens
Characteristics reference: Normal human male genomic DNA
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name LS411 genomic DNA
Organism Homo sapiens
Characteristics cell type: colorectal cancer
cell line: LS411
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/2006-08/69938.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 6499 3158 808 984 5691 2174 6551 3166 827 1017 5743 2182 0 0 1286 705 263 384 100 100 100 97 7865 7925 2.618 .382 .38 .39 .39 .14 86 333 .49 .99 100 2660 6420 37 47 33 43 0 2185 681 1504 .264 2190 1510 3.784 .263 -1.92 -1.928
2 8366 6797 803 965 7563 5832 8557 7160 845 1011 7754 6195 0 0 2075 2146 391 525 100 98 98 95 13395 13949 1.297 .771 .799 .74 .8 .23 58 279 .82 .99 80 2800 6430 39 47 48 56 0 4702 668 4035 .533 4954 4286 1.874 .553 -.906 -.855
3 8755 7347 772 959 7983 6388 8910 7393 791 989 8138 6434 0 0 1498 1235 264 344 100 100 100 100 14371 14572 1.25 .8 .791 .8 .81 .15 86 295 .84 .99 100 2940 6430 38 48 61 71 0 5083 663 4419 .554 5115 4451 1.806 .547 -.853 -.87
4 7757 7156 763 945 6994 6211 7924 7182 793 985 7161 6237 0 0 1766 1512 273 330 100 100 100 100 13205 13398 1.126 .888 .871 .92 .91 .24 61 364 .93 .99 90 3090 6430 38 47 76 85 0 4951 654 4297 .614 4969 4315 1.628 .603 -.703 -.731
5 7101 5864 753 909 6348 4955 7075 5981 768 972 6322 5072 0 0 1374 1274 286 340 100 100 100 100 11303 11394 1.281 .781 .802 .78 .76 .2 80 321 .83 .99 100 3240 6430 38 48 91 101 0 4057 629 3428 .54 4138 3509 1.852 .555 -.889 -.849
6 7660 6833 758 942 6902 5891 7764 6798 784 1007 7006 5856 0 0 1472 1446 276 346 100 100 100 100 12793 12862 1.172 .854 .836 .85 .84 .16 48 313 .9 .99 80 3390 6430 39 47 107 115 0 4727 652 4076 .59 4703 4051 1.693 .578 -.76 -.79
7 6813 6457 760 918 6053 5539 6885 6504 800 963 6125 5586 0 0 1816 1648 282 337 100 100 100 100 11592 11711 1.093 .915 .912 .93 .9 .24 136 216 .96 .99 130 3540 6430 36 49 119 132 0 4467 635 3832 .633 4500 3865 1.58 .631 -.66 -.664
8 6208 5911 788 925 5420 4986 6202 5845 825 1000 5414 4920 0 0 1078 1068 302 576 100 100 100 100 10406 10334 1.087 .92 .909 .94 .93 .25 97 228 .96 .99 110 3670 6430 37 48 133 144 0 4089 640 3449 .636 4044 3404 1.571 .629 -.652 -.67
9 6048 7691 815 957 5233 6734 6049 7772 857 1003 5234 6815 0 0 1208 1359 320 540 100 100 100 100 11967 12049 .777 1.287 1.302 1.33 1.37 .35 86 273 1.27 .99 100 3820 6430 38 48 149 159 0 5321 662 4659 .89 5377 4715 1.123 .901 -.168 -.151
10 9740 8438 801 896 8939 7542 10248 8931 821 917 9447 8035 0 0 2552 2326 278 303 100 99 100 99 16481 17482 1.185 .844 .851 .85 .88 .23 72 297 .88 .99 90 3970 6420 37 46 164 173 0 5838 620 5218 .584 6179 5559 1.713 .588 -.777 -.765
11 3842 4715 799 928 3043 3787 3789 4865 805 963 2990 3937 0 0 890 1162 261 336 100 100 100 100 6830 6927 .804 1.244 1.317 1.32 1.23 .56 104 331 1.23 .99 110 4110 6420 36 47 177 188 0 3262 642 2620 .861 3366 2724 1.161 .911 -.216 -.135
12 5747 6451 790 967 4957 5484 5627 6323 827 1003 4837 5356 0 0 1376 1289 293 333 100 100 100 100 10441 10193 .904 1.106 1.107 1.15 1.14 .3 37 342 1.11 .99 70 4260 6440 40 47 194 201 0 4463 669 3794 .765 4374 3705 1.307 .766 -.386 -.384
13 6103 9330 779 961 5324 8369 6065 9278 810 993 5286 8317 0 0 1535 2025 262 342 100 100 100 100 13693 13603 .636 1.572 1.573 1.62 1.59 .37 104 302 1.53 .99 110 4400 6430 37 48 206 217 0 6455 665 5790 1.088 6419 5754 .92 1.089 .121 .122
14 8969 7566 778 973 8191 6593 8979 7624 799 1011 8201 6651 0 0 1198 1120 244 356 100 100 100 100 14784 14852 1.242 .805 .811 .8 .81 .15 86 256 .85 .99 100 4550 6430 38 48 222 232 0 5234 673 4561 .557 5275 4601 1.796 .561 -.845 -.834
15 4247 5619 841 1035 3406 4584 4153 5658 848 1042 3312 4623 0 0 896 1023 245 322 99 100 99 100 7990 7935 .743 1.346 1.396 1.43 1.41 .63 166 174 1.32 .99 140 4690 6430 36 50 234 248 0 3887 716 3171 .931 3914 3198 1.074 .966 -.103 -.05
16 20945 27847 894 934 20051 26913 21010 28692 873 969 20116 27758 0 0 4262 5766 265 321 100 100 100 100 46964 47874 .745 1.342 1.38 1.35 1.37 .26 140 215 1.33 1 130 4840 6430 36 49 249 262 0 19266 646 18619 .929 19850 19204 1.077 .955 -.107 -.067
17 6192 9764 900 918 5292 8846 6232 10064 919 970 5332 9146 0 0 1406 1941 292 329 100 100 100 100 14138 14478 .598 1.672 1.715 1.74 1.72 .44 86 258 1.58 .99 100 4990 6430 38 48 266 276 0 6755 635 6120 1.156 6963 6328 .865 1.187 .21 .247
18 7728 11755 916 964 6812 10791 8032 12158 952 1003 7116 11194 0 0 1867 2938 314 343 99 100 99 100 17603 18310 .631 1.584 1.573 1.84 1.61 2.08 72 292 1.52 .99 90 5140 6430 38 47 281 290 0 8133 667 7466 1.096 8411 7744 .912 1.088 .132 .122
19 16061 24310 873 995 15188 23315 16185 25393 894 1008 15312 24398 0 0 3773 5537 299 331 100 100 100 100 38503 39710 .651 1.535 1.593 1.54 1.59 .2 86 307 1.51 1 100 5280 6430 38 48 295 305 0 16818 688 16130 1.062 17568 16879 .942 1.102 .087 .141
20 6179 9773 777 974 5402 8799 6431 10334 793 1006 5654 9360 0 0 1861 2514 264 317 100 100 100 100 14201 15014 .614 1.629 1.655 1.72 1.67 .45 51 364 1.56 .99 80 5420 6440 40 48 310 318 0 6761 674 6087 1.127 7149 6476 .887 1.145 .172 .196

Total number of rows: 41472

Table truncated, full table size 9924 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap