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Sample GSM69969 Query DataSets for GSM69969
Status Public on Aug 16, 2005
Title J99-A7-4 vs Tigr/Astra references (250 ug).
Sample type genomic
 
Channel 1
Source name 250 ng Tigr/Astra genomic DNA
Organism Helicobacter pylori
Characteristics 250 ng Tigr/Astra genomic DNA
Extracted molecule genomic DNA
Label Cy3
 
Channel 2
Source name 250 ng J99-A7 genomic DNA
Organism Helicobacter pylori
Characteristics 250 ng J99-A7 genomic DNA
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18212.gif
Data processing VALUE is Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Aug 15, 2005
Last update date Sep 22, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) array@genome.stanford.edu
Phone 650-498-6012
URL http://genome-www5.stanford.edu/
Department Stanford University, School of Medicine
Street address 300 Pasteur Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL15
Series (1)
GSE3137 H. pilory diversity in human

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 LOG_RAT2N_MEDIANs 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 LOG_RAT2N_MEDIAN of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized LOG_RAT2N_MEDIAN of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized LOG_RAT2N_MEDIAN 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 LOG_RAT2N_MEDIAN of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized LOG_RAT2N_MEDIAN 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
VALUE 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
LOG_RAT2N_MEDIAN 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 VALUE LOG_RAT2N_MEDIAN
1 33230 30575 896 915 32334 29660 33818 31553 971 988 32922 30638 0 0 4927 5471 723 579 100 100 100 100 61994 63560 1.09 .917 .931 .912 .923 1.163 52 412 .934 .97 90 1300 13100 41 50 33 42 0 35803 1071 34732 1.074 36949 35877 .931 1.09 .103 .124
2 18643 3251 835 804 17808 2447 19235 3154 852 832 18400 2350 0 0 3326 891 192 223 100 100 100 100 20255 20750 7.277 .137 .128 .13 .14 1.399 52 420 .131 .92 90 1550 13100 41 50 58 67 0 3807 941 2865 .161 3693 2752 6.215 .15 -2.636 -2.741
3 24655 23647 838 798 23817 22849 24797 24287 850 811 23959 23489 0 0 2798 3936 165 172 100 100 100 100 46666 47448 1.042 .959 .98 .949 .986 1.153 52 412 .97 .98 90 1790 13090 40 49 82 91 0 27691 934 26756 1.123 28440 27506 .89 1.148 .168 .199
4 1031 1124 784 776 247 348 692 685 811 813 -92 -91 0 0 969 1346 313 378 15 16 13 15 595 -183 .71 1.409 null 1.128 1.293 2.797 80 656 1.372 .85 110 2030 13100 40 51 105 116 -100 1316 909 408 1.65 802 -107 .606 null .722 null
5 1643 1820 787 776 856 1044 778 768 800 787 -9 -8 0 0 1965 2477 140 166 30 35 27 27 1900 -17 .82 1.22 null 1.202 1.268 2.863 80 656 1.272 .93 110 2270 13100 40 51 129 140 -100 2131 909 1223 1.428 899 -9 .7 null .514 null
6 13251 8654 819 773 12432 7881 13451 8711 838 789 12632 7938 0 0 1505 1112 167 178 100 100 100 100 20313 20570 1.577 .634 .628 .632 .64 1.141 156 1127 .618 .98 150 2520 13100 38 53 152 167 0 10134 905 9229 .742 10201 9295 1.347 .736 -.43 -.442
7 2581 2515 790 741 1791 1774 1434 1298 806 753 644 557 0 0 2348 2285 148 168 73 71 65 60 3565 1201 1.01 .991 .865 .955 1.002 2.408 80 634 .98 .94 110 2750 13100 40 51 177 188 -100 2945 868 2077 1.16 1520 652 .862 1.013 .214 .018
8 1330 1275 762 729 568 546 741 742 785 758 -21 13 0 0 1079 1018 201 251 41 36 32 31 1114 -8 1.04 .961 null 1.151 1.066 2.262 80 648 .969 .93 110 2990 13100 40 51 201 212 -100 1493 854 639 1.126 869 15 .888 null .171 null
9 16595 14085 783 741 15812 13344 18444 15338 793 747 17661 14597 0 0 7673 6639 132 147 100 100 100 100 29156 32258 1.185 .844 .827 .814 .825 1.772 80 544 .846 .97 100 3240 13100 41 51 227 237 0 16494 868 15626 .988 17961 17093 1.012 .968 -.017 -.047
10 1586 1698 822 760 764 938 921 924 829 771 99 164 0 0 1484 1768 151 156 42 51 32 32 1702 263 .814 1.228 1.657 1.053 1.156 3.655 80 656 1.205 .92 110 3470 13110 41 52 249 260 -100 1988 890 1098 1.438 1082 192 .696 1.94 .524 .956
11 2681 2596 871 786 1810 1810 1070 1020 890 811 199 234 0 0 2881 2883 169 187 55 52 43 43 3620 433 1 1 1.176 1.087 1.092 3.27 80 656 1.002 .91 110 3700 13110 41 52 272 283 -100 3040 920 2120 1.171 1194 274 .854 1.377 .228 .461
12 9713 2016 938 879 8775 1137 9942 2025 961 896 9004 1146 0 0 1559 404 198 210 100 98 100 94 9912 10150 7.718 .13 .127 .121 .127 1.452 156 1140 .13 .89 150 3950 13100 38 53 295 310 0 2361 1029 1331 .152 2371 1342 6.591 .149 -2.72 -2.746
13 9841 15388 1004 971 8837 14417 9750 14617 1017 980 8746 13646 0 0 3183 4726 173 206 100 100 100 100 23254 22392 .613 1.631 1.56 1.659 1.561 1.454 80 552 1.663 .95 100 4190 13110 42 52 322 332 0 18019 1137 16882 1.91 17117 15979 .523 1.827 .934 .87
14 9009 6791 1036 1020 7973 5771 9179 6454 1085 1076 8143 5434 0 0 5087 3929 360 464 97 92 93 87 13744 13577 1.382 .724 .667 .709 .715 1.426 80 538 .758 .96 100 4430 13100 41 51 346 356 0 7952 1194 6758 .848 7558 6363 1.18 .781 -.239 -.356
15 3187 1556 1008 1027 2179 529 1232 978 1022 1041 224 -49 0 0 3642 1238 169 213 52 36 47 33 2708 175 4.119 .243 null .715 .609 3.394 80 656 .313 .92 110 4660 13120 42 53 368 379 -100 1822 1203 619 .284 1145 -57 3.518 null -1.815 null
16 2534 2175 981 984 1553 1191 1449 1233 990 1014 468 249 0 0 2605 2257 166 200 63 51 55 41 2744 717 1.304 .767 .532 .717 .771 2.44 80 656 .843 .95 110 4900 13120 42 53 392 403 -100 2547 1152 1395 .898 1444 292 1.114 .623 -.155 -.683
17 2744 4053 952 976 1792 3077 1878 2770 977 990 926 1794 0 0 2343 3962 246 225 85 88 75 80 4869 2720 .582 1.717 1.937 1.731 1.77 2.069 80 656 1.704 .97 110 5140 13120 42 53 416 427 -100 4746 1143 3603 2.011 3244 2101 .497 2.269 1.008 1.182
18 2383 1911 819 816 1564 1095 1112 895 835 827 293 79 0 0 2748 2232 163 167 58 45 47 41 2659 372 1.428 .7 .27 1.049 1.147 3.704 80 656 .769 .87 110 1310 13330 63 74 33 44 -100 2238 956 1282 .82 1048 93 1.22 .316 -.287 -1.663
19 6422 4586 755 725 5667 3861 4744 2945 772 745 3989 2220 0 0 4904 3244 130 164 100 100 98 98 9528 6209 1.468 .681 .557 .718 .744 1.722 52 340 .657 .94 80 1550 13340 66 74 59 67 0 5370 849 4521 .798 3449 2600 1.253 .652 -.326 -.618
20 998 828 762 722 236 106 705 613 773 732 -57 -109 0 0 820 664 133 160 21 17 17 12 342 -166 2.226 .449 null .927 1.002 3.406 80 614 .762 .69 110 1790 13340 64 75 81 92 -100 970 845 124 .526 718 -128 1.901 null -.927 null

Total number of rows: 4608

Table truncated, full table size 1135 Kbytes.




Supplementary data files not provided
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