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Sample GSM478 Query DataSets for GSM478
Status Public on Jul 25, 2001
Title Hp1 vs. TIGR/Astra ref. genomic DNA; amino-allyl labeling
Sample type genomic
 
Channel 1
Source name 1ug Tigr genomic DNA, 1ug Astra genomic DNA
Organism Helicobacter pylori
Extracted molecule genomic DNA
 
Channel 2
Source name 2 ug Hp1 genomic DNA
Organism Helicobacter pylori
Extracted molecule genomic DNA
 
 
Description Category: Strain comparison
Subcategory: Strain Comparison
Scanning Software: ScanAlyze
Software version: 2.42
Scanning parameters:
Lot batch = hp2042
 
Submission date Jul 25, 2001
Last update date Nov 21, 2005
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)
GSE6 Genetic diversity among Helicobacter pylori strains

Data table header descriptions
ID_REF
CH1B_MEAN mean channel 1 background
CH1B_MEDIAN median channel 1 background
CH1D_MEAN difference between CH1I_MEAN and CH1B_MEAN
CH2I_MEAN mean channel 2 signal
CH2D_MEAN difference of CH2I_MEAN and CH2B_MEAN
CH2B_MEAN mean of channel 2 background
CH2B_MEDIAN median of channel 2 background
CH2BN_MEDIAN normalized CH2B_MEDIAN
CH2DN_MEAN normalized CH2D_MEAN
CH2IN_MEAN normalized CH2I_MEAN
CORR simple correlation coefficient of channel 1 and channel 2 pixels
FLAG user defined flag (default=0)
VALUE same as UNF_VALUE but with flagged values removed
PIX_RAT2_MEDIAN
PERGTBCH1I_1SD standard deviation of fraction of pixels greater than CH1B_MEAN
PERGTBCH2I_1SD standard deviation of fraction of pixels greater than CH2B_MEAN
RAT1_MEAN ratio of CH1D_MEAN to CH2D_MEAN
RAT1N_MEAN ratio of CH1DN_MEAN to CH2DN_MEAN
RAT2_MEAN ratio of CH2D_MEAN to CH1D_MEAN
RAT2N_MEAN ratio of CH2DN_MEAN and CH1DN_MEAN
REGR slope of the simple regression line of channel 2 to channel 1 pixels
TOT_BPIX total number of background pixels
TOT_SPIX total number of signal (spot) pixels
TOP vertical, short-axis spot ellipse minimum pixel coordinate
BOT vertical, short-axis spot ellipse maximum pixel coordinate
LEFT horizontal, long-axis spot ellipse minimum pixel coordinate
RIGHT horizontal, long-axis spot ellipse maximum pixel coordinate
UNF_VALUE aka LOG_RAT2N_MEAN, or log2 of ratio of CH2DN_MEAN and CH1DN_MEAN

Data table
ID_REF CH1B_MEAN CH1B_MEDIAN CH1D_MEAN CH2I_MEAN CH2D_MEAN CH2B_MEAN CH2B_MEDIAN CH2BN_MEDIAN CH2DN_MEAN CH2IN_MEAN CORR FLAG VALUE PIX_RAT2_MEDIAN PERGTBCH1I_1SD PERGTBCH2I_1SD RAT1_MEAN RAT1N_MEAN RAT2_MEAN RAT2N_MEAN REGR TOT_BPIX TOT_SPIX TOP BOT LEFT RIGHT UNF_VALUE
1 697 599 617 9 982 608 733 10 743 .01 0 1.237 0 1 .013 1523 112 78 90 44 56
2 779 632 4 634 1061 644 776 764 -.092 0 .56 2 3 -.099 1466 112 78 90 68 80
3 708 640 8893 8215 7538 707 677 816 9082 9898 0 0 .03 .852 97 96 1.18 .979 .848 1.021 0 1441 216 72 88 90 107 .03
4 670 629 335 833 167 691 666 802 202 1004 .651 0 -.73 .628 35 23 2.006 1.658 .499 .603 .4 1482 112 76 88 117 129 -.73
5 703 626 349 856 178 706 678 817 214 1031 .555 0 -.706 .596 37 23 1.961 1.631 .51 .613 .313 1507 112 76 88 141 153 -.706
6 779 660 7431 4324 3617 751 707 852 4358 5210 0 0 -.77 .478 90 82 2.054 1.705 .487 .586 0 1508 112 75 87 165 177 -.77
7 691 661 781 1322 636 705 686 827 766 1593 .867 0 -.028 .927 54 51 1.228 1.02 .814 .981 .734 1510 112 74 86 189 201 -.028
8 660 642 379 797 126 685 671 808 152 960 .602 0 -1.318 .49 41 16 3.008 2.493 .332 .401 .243 1510 112 74 86 213 225 -1.318
9 698 659 3947 4402 3681 745 721 869 4435 5304 0 0 .168 .93 85 84 1.072 .89 .933 1.124 0 1483 112 73 85 237 249 .168
10 712 676 733 1319 575 766 744 896 693 1589 .825 0 -.081 .876 53 52 1.275 1.058 .784 .945 .696 1455 112 72 84 261 273 -.081
11 717 670 861 1455 734 749 721 869 884 1753 .757 0 .038 .918 66 58 1.173 .974 .852 1.027 .728 1491 112 72 84 285 297 .038
12 787 698 5191 1890 1178 737 712 858 1419 2277 0 0 -1.871 .228 91 71 4.407 3.658 .227 .273 0 1511 112 71 83 309 321 -1.871
13 830 735 3264 3108 2375 765 733 883 2862 3745 .827 0 -.19 .768 96 96 1.374 1.14 .728 .877 .529 1511 112 70 82 333 345 -.19
14 853 774 6928 6086 5285 842 801 965 6368 7333 0 0 -.122 .764 99 91 1.311 1.088 .763 .919 0 1504 112 70 82 357 369 -.122
15 862 793 633 1498 664 866 834 1005 800 1805 .765 0 .338 1.136 58 60 .953 .791 1.049 1.264 .655 1489 112 69 81 381 393 .338
16 766 724 2727 3135 2358 792 777 936 2841 3777 .879 0 .059 .917 60 63 1.156 .96 .865 1.042 .704 1503 112 69 81 405 417 .059
17 691 660 4601 4798 4086 727 712 858 4923 5781 0 0 .098 .906 78 77 1.126 .935 .888 1.07 0 1553 112 66 78 429 441 .098
18 683 619 729 1177 544 675 633 763 655 1418 .797 0 -.154 .822 50 49 1.34 1.113 .746 .898 .536 1509 112 102 114 45 57 -.154
19 768 672 5098 5419 4726 763 693 835 5694 6529 0 0 .16 .932 93 99 1.079 .895 .927 1.117 0 1489 112 101 113 69 81 .16
20 731 676 535 1013 303 752 710 855 365 1220 .623 0 -.552 .676 50 33 1.766 1.466 .566 .682 .311 1494 112 101 113 93 105 -.552

Total number of rows: 4608

Table truncated, full table size 568 Kbytes.




Supplementary data files not provided

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