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Sample GSM477 Query DataSets for GSM477
Status Public on Jul 25, 2001
Title 342S 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 342S 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 = hp2041
 
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
1 608 594 716 3 727 713 621 3 624 -.015 0 .652 1 0 -.008 1524 112 32 44 38 50
2 675 631 701 762 713 621 -10 611 -.028 0 .235 0 0 -.015 1476 112 33 45 62 74
3 678 661 4114 6160 5406 776 754 657 4710 5367 0 0 .195 1.274 87 89 .761 .873 1.314 1.145 0 1405 216 31 47 84 101 .195
4 659 650 206 955 163 793 792 690 142 832 .698 0 -.537 .743 28 10 1.264 1.451 .791 .689 .435 1467 112 33 45 110 122 -.537
5 670 653 197 814 34 777 780 680 30 709 .657 0 -2.733 .333 19 0 5.794 6.651 .173 .15 .252 1509 112 33 45 134 146 -2.733
6 708 679 3535 2866 2062 813 804 700 1796 2497 .895 0 -.977 .584 96 88 1.714 1.968 .583 .508 .497 1508 112 34 46 158 170 -.977
7 702 674 402 1159 337 831 822 716 294 1010 .895 0 -.453 .937 35 29 1.193 1.369 .838 .73 .636 1516 112 34 46 183 195 -.453
8 686 667 372 823 47 774 776 676 41 717 .784 0 -3.183 .432 41 15 7.915 9.085 .126 .11 .495 1510 112 34 46 207 219 -3.183
9 689 675 1780 2925 2168 756 757 660 1889 2548 .942 0 .086 1.201 73 77 .821 .942 1.218 1.061 1.065 1507 112 34 46 231 243 .086
10 704 678 243 874 123 778 751 654 107 761 .768 0 -1.181 .624 32 16 1.976 2.268 .506 .441 .745 1483 112 34 46 255 267 -1.181
11 747 708 385 1033 234 846 799 696 204 900 .85 0 -.917 .666 34 22 1.645 1.888 .608 .53 .466 1442 112 35 47 279 291 -.917
12 793 751 2444 1034 242 823 792 690 211 901 .776 0 -3.535 .101 81 20 10.099 11.592 .099 .086 .078 1493 112 35 47 303 315 -3.535
13 773 753 1349 1005 219 806 786 685 191 876 .739 0 -2.822 .213 78 33 6.16 7.07 .162 .141 .225 1509 112 35 47 327 339 -2.822
14 800 766 2679 4481 3611 900 870 758 3146 3904 .798 0 .232 1.345 88 95 .742 .852 1.348 1.174 .951 1514 112 35 47 351 363 .232
15 805 780 252 1169 287 910 882 768 250 1018 .838 0 -.011 1.137 28 18 .878 1.008 1.139 .992 .676 1482 112 36 48 376 388 -.011
16 793 780 1079 1874 998 880 876 763 869 1633 .9 0 -.311 .962 58 58 1.081 1.241 .925 .806 .744 1500 112 36 48 400 412 -.311
17 778 764 2023 2809 2006 813 803 700 1748 2447 .893 0 -.211 .994 75 75 1.008 1.158 .992 .864 .876 1535 112 36 48 424 436 -.211
18 701 639 581 1038 267 830 771 672 233 904 .687 0 -1.321 .733 41 28 2.176 2.498 .46 .4 .163 1508 112 56 68 38 50 -1.321
19 753 681 2718 4388 3591 865 797 694 3129 3823 .891 0 .203 1.416 85 92 .757 .869 1.321 1.151 .975 1490 112 57 69 62 74 .203
20 702 678 278 900 84 835 816 711 73 784 .638 0 -1.926 .414 26 3 3.31 3.799 .302 .263 .243 1457 112 57 69 86 98 -1.926

Total number of rows: 4608

Table truncated, full table size 554 Kbytes.




Supplementary data files not provided

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