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Sample GSM476 Query DataSets for GSM476
Status Public on Jul 25, 2001
Title T2 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 T2 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 = hp2040
 
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
1 676 658 349 376 351 304 -2 302 -.132 0 1.153 0 0 -.075 1522 112 43 55 42 54
2 774 747 18 447 493 468 406 -18 387 .106 0 .429 0 1 .046 1477 112 43 55 66 78
3 857 820 4850 6347 5765 626 582 504 4997 5501 0 0 .043 1.152 75 82 .841 .971 1.189 1.03 0 1405 216 41 57 88 105 .043
4 860 822 262 758 142 652 616 534 123 657 .546 0 -1.09 .486 24 16 1.845 2.129 .542 .47 .31 1467 112 43 55 114 126 -1.09
5 872 842 163 674 53 632 621 538 46 584 .301 0 -1.827 .609 14 5 3.075 3.548 .325 .282 .141 1509 112 43 55 138 150 -1.827
6 925 870 5364 2746 2101 655 645 559 1821 2380 0 0 -1.559 .396 90 88 2.553 2.946 .392 .339 0 1509 112 43 55 162 174 -1.559
7 855 824 466 1105 494 672 611 530 428 958 .574 0 -.122 .885 35 47 .943 1.088 1.06 .919 .666 1509 112 43 55 186 198 -.122
8 812 788 246 648 53 662 595 516 46 562 .26 0 -2.421 .626 21 8 4.642 5.355 .215 .187 .171 1509 112 43 55 210 222 -2.421
9 804 763 2541 3635 3083 582 552 478 2672 3150 .876 0 .073 1.322 80 93 .824 .951 1.213 1.052 .977 1482 112 43 55 234 246 .073
10 782 748 344 776 274 535 502 435 237 673 .845 0 -.535 .756 33 42 1.255 1.449 .797 .69 .62 1452 112 43 55 258 270 -.535
11 778 743 481 859 392 521 467 405 340 745 .744 0 -.502 .926 41 48 1.227 1.416 .815 .706 .52 1457 112 43 55 283 295 -.502
12 855 797 3699 843 336 554 507 439 291 731 .769 0 -3.667 .097 82 56 11.009 12.702 .091 .079 .081 1493 112 43 55 307 319 -3.667
13 868 824 1305 2394 1807 621 587 509 1566 2075 .744 0 .263 1.299 65 79 .722 .833 1.385 1.2 .939 1509 112 43 55 331 343 .263
14 890 836 4385 5704 5073 699 631 547 4397 4944 0 0 .004 1.164 87 96 .864 .997 1.157 1.003 0 1509 112 43 55 355 367 .004
15 857 807 267 1028 414 675 614 532 359 891 .396 0 .426 1.38 18 48 .645 .744 1.551 1.344 .354 1509 112 43 55 379 391 .426
16 797 777 1480 2423 1837 607 586 508 1592 2100 .892 0 .105 1.173 57 62 .806 .93 1.241 1.076 1.042 1509 112 43 55 403 415 .105
17 935 779 3089 3345 2761 734 584 506 2393 2899 .888 0 -.368 .898 66 67 1.119 1.291 .894 .775 .733 1534 112 43 55 427 439 -.368
18 758 701 505 840 423 483 417 361 367 728 .835 0 -.462 .886 38 50 1.194 1.377 .838 .726 .625 1509 112 67 79 42 54 -.462
19 832 794 3646 3754 3226 573 528 458 2796 3254 .891 0 -.383 .9 91 99 1.13 1.304 .885 .767 .787 1489 112 67 79 66 78 -.383
20 849 824 316 710 102 631 608 527 88 615 .782 0 -1.838 .522 25 16 3.098 3.574 .323 .28 .392 1468 112 67 79 90 102 -1.838

Total number of rows: 4608

Table truncated, full table size 559 Kbytes.




Supplementary data files not provided

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