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GEO Accession viewer

2024-05-21 21:02| 来源: 网络整理| 查看: 265

Sample GSM78740 Query DataSets for GSM78740 Status Public on Oct 20, 2005 Title AR28 vs Tigr/Astra Reference 2 Sample type genomic   Channel 1 Source name 1ug Tigr genomic DNA + 1ug Astra genomic DNA Organism Helicobacter pylori Characteristics 1ug Tigr genomic DNA + 1ug Astra genomic DNA Extracted molecule genomic DNA Label Cy3   Channel 2 Source name 2 ug AR28 genomic DNA Organism Helicobacter pylori Characteristics 2 ug AR28 genomic DNA Extracted molecule genomic DNA Label Cy5     Description Simple annotation: Genomic DNA, Strain ComparisonImage: http://smd.stanford.edu/MicroArray/gifs/2000-12/11921.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 Oct 19, 2005 Last update date Feb 20, 2008 Organization Stanford Microarray Database (SMD) E-mail(s) [email protected] 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) GSE3479 Helicobacter pylori bacterial populations 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 same as UNF_VALUE but with flagged values removed 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 UNF_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 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 UNF_VALUE 1 5789 5001 655 902 5134 4099 null null 707 931 null null null null null null null null 96 96 null null null null 1.253 .798 null null .78 null 80 552 .799 .98 null null null 82 92 64 74 0 5556 1002 4554 .887 null null 1.127 null -.173 null -.173 2 2809 2004 611 853 2198 1151 null null 622 861 null null null null null null null null 98 97 null null null null 1.91 .524 null null .522 null 80 656 .521 .97 null null null 81 92 87 98 0 2226 947 1279 .582 null null 1.719 null -.781 null -.781 3 3787 3482 595 825 3192 2657 null null 608 832 null null null null null null null null 98 97 null null null null 1.201 .832 null null .817 null 80 560 .828 .98 null null null 82 92 112 122 0 3868 916 2952 .925 null null 1.081 null -.113 null -.113 4 1297 1257 586 776 711 481 null null 608 785 null null null null null null null null 84 62 null null null null 1.478 .677 null null .724 null 32 236 .76 .91 null null null 82 89 141 148 0 1396 862 534 .751 null null 1.331 null -.413 null -.413 5 981 1101 667 816 314 285 null null 717 858 null null null null null null null null 37 40 null null null null 1.102 .908 null null .954 null 32 236 .852 .91 null null null 82 89 165 172 0 1223 906 317 1.01 null null .991 null .014 null .014 6 5580 3529 654 821 4926 2708 null null 670 833 null null null null null null null null 100 100 null null null null 1.819 .55 null null .551 null 80 652 .554 .98 null null null 81 92 183 194 0 3921 912 3009 .611 null null 1.637 null -.711 null -.711 7 1183 1197 776 922 407 275 null null 926 1021 null null null null null null null null 25 16 null null null null 1.48 .676 null null .996 null 12 104 .785 .95 null null null 83 88 212 217 0 1330 1024 306 .752 null null 1.33 null -.411 null -.411 8 1082 1125 645 882 437 243 null null 883 1070 null null null null null null null null 8 8 null null null null 1.798 .556 null null .415 null 12 104 .936 .96 null null null 83 88 237 242 0 1250 980 270 .618 null null 1.619 null -.695 null -.695 9 4751 4637 663 864 4088 3773 null null 688 886 null null null null null null null null 100 100 null null null null 1.083 .923 null null .918 null 52 420 .944 .98 null null null 81 90 257 266 0 5152 960 4192 1.025 null null .975 null .036 null .036 10 1340 1477 630 828 710 649 null null 648 842 null null null null null null null null 68 62 null null null null 1.094 .914 null null 1.138 null 32 160 .919 .95 null null null 82 88 285 291 0 1641 920 721 1.015 null null .985 null .022 null .022 11 1271 1379 678 877 593 502 null null 768 950 null null null null null null null null 34 37 null null null null 1.181 .847 null null .891 null 32 230 .968 .99 null null null 81 88 307 314 0 1532 974 558 .941 null null 1.063 null -.088 null -.088 12 3024 1228 672 859 2352 369 null null 688 868 null null null null null null null null 98 57 null null null null 6.374 .157 null null .165 null 80 552 .17 .71 null null null 81 91 329 339 0 1364 954 410 .174 null null 5.737 null -2.52 null -2.52 13 2395 1626 652 898 1743 728 null null 671 910 null null null null null null null null 83 75 null null null null 2.394 .418 null null .426 null 80 656 .409 .9 null null null 80 91 352 363 0 1806 997 809 .464 null null 2.155 null -1.107 null -1.107 14 3286 3571 648 949 2638 2622 null null 665 965 null null null null null null null null 93 92 null null null null 1.006 .994 null null 1.025 null 80 552 .978 .98 null null null 81 91 378 388 0 3967 1054 2913 1.104 null null .906 null .143 null .143 15 965 1126 632 977 333 149 null null 879 1137 null null null null null null null null 9 9 null null null null 2.235 .447 null null .744 null 32 220 .759 .97 null null null 80 87 404 411 0 1251 1085 166 .498 null null 2.006 null -1.004 null -1.004 16 1394 1671 640 979 754 692 null null 694 1009 null null null null null null null null 65 50 null null null null 1.09 .918 null null .873 null 32 220 .886 .96 null null null 80 87 427 434 0 1856 1087 769 1.02 null null .98 null .028 null .028 17 1729 1915 642 976 1087 939 null null 692 1010 null null null null null null null null 63 71 null null null null 1.158 .864 null null .837 null 52 400 .827 .97 null null null 79 88 450 459 0 2127 1084 1043 .96 null null 1.042 null -.06 null -.06 18 1565 1616 640 890 925 726 null null 675 911 null null null null null null null null 82 82 null null null null 1.274 .785 null null .861 null 52 340 .742 .89 null null null 107 115 67 75 0 1795 988 807 .872 null null 1.146 null -.197 null -.197 19 1891 1907 662 893 1229 1014 null null 717 928 null null null null null null null null 96 93 null null null null 1.212 .825 null null .762 null 32 176 .817 .91 null null null 107 113 91 97 0 2118 992 1126 .916 null null 1.091 null -.126 null -.126 20 1102 1197 627 832 475 365 null null 645 853 null null null null null null null null 68 59 null null null null 1.301 .768 null null .775 null 32 236 .675 .84 null null null 106 113 115 122 0 1330 924 406 .855 null null 1.17 null -.226 null -.226 Total number of rows: 4608

Table truncated, full table size 1166 Kbytes.

Supplementary data files not provided


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