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Sample GSM504 Query DataSets for GSM504
Status Public on Jul 25, 2001
Title Astra genomic DNA vs TIGR/Astra reference, trial 1
Sample type genomic
 
Channel 1
Source name 2 ug Astra genomic DNA
Organism Helicobacter pylori
Extracted molecule genomic DNA
 
Channel 2
Source name 0.7 ug TIGR genomic DNA, 0.7 ug Astra genomic DNA
Organism Helicobacter pylori
Extracted molecule genomic DNA
 
 
Description Category: Genomic DNA
Subcategory: Strain Comparison
Astra genomic DNA vs TIGR/Astra reference, trail 1
Scanning Software: GenePix
Software version: Pro
Scanning parameters:
Lot batch = hp4067
 
Submission date Jul 25, 2001
Last update date May 27, 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 (2)
GSE6 Genetic diversity among Helicobacter pylori strains
GSE3479 Helicobacter pylori bacterial populations

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 aka LOG_RAT2N_MEAN, or log2 of ratio of CH2DN_MEAN and CH1DN_MEAN
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

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
1 469 461 9216 9256 8687 572 569 592 9049 9641 .94 0 -.026 .899 100 100 1.061 1.018 .943 .982 .896 306 52 64 72 68 76
2 448 443 4175 1284 754 542 530 552 785 1337 .89 0 -2.411 .21 100 92 5.537 5.318 .181 .188 .15 332 52 62 70 92 100
3 498 453 2837 3467 2882 608 585 609 3002 3611 .9 0 .082 1.027 80 96 .984 .945 1.016 1.058 .945 412 52 61 70 115 124
4 451 448 51 688 123 570 565 588 128 716 .21 -100 1.328 1.758 38 47 .415 .398 2.412 2.51 .336 552 80 61 71 140 150
5 456 451 36 682 102 584 580 604 106 710 .21 -100 1.558 1.447 35 43 .353 .34 2.833 2.944 .369 552 80 61 71 164 174
6 553 523 2286 1485 795 712 690 718 828 1546 .87 0 -1.465 .374 100 93 2.875 2.761 .348 .362 .327 160 32 62 68 190 196
7 532 523 67 720 750 742 772 750 .42 -100 1.134 27 11 .467 552 80 61 71 212 222
8 532 525 159 861 120 746 741 771 125 896 .7 -100 -.347 1.468 36 26 1.325 1.272 .755 .786 .822 552 80 61 71 236 246
9 571 551 3778 4423 3644 797 779 811 3796 4607 .87 0 .007 .988 100 96 1.037 .995 .965 1.005 .858 213 32 60 67 262 269
10 609 548 114 818 37 858 781 813 39 852 .78 -100 -1.547 1.42 2 2 3.081 2.923 .325 .342 1.208 552 80 60 70 284 294
11 595 583 124 856 69 799 787 819 72 891 .59 -100 -.784 1.248 27 20 1.797 1.722 .556 .581 .618 552 80 60 70 308 318
12 644 631 8564 1271 455 827 816 850 473 1323 .79 0 -4.178 .057 100 59 18.822 18.106 .053 .055 .058 332 52 61 69 334 342
13 610 607 2057 3303 2452 853 851 886 2554 3440 .88 0 .312 1.222 94 92 .839 .805 1.192 1.242 1.037 420 52 61 70 357 366
14 599 592 3621 4379 3555 823 824 858 3703 4561 .95 0 .032 1.043 100 100 1.019 .978 .982 1.023 .977 230 32 61 68 382 389
15 605 592 3423 2130 1262 859 868 904 1314 2218 .82 0 -1.381 .416 91 83 2.712 2.605 .369 .384 .368 90 12 61 66 406 411
16 613 609 354 1141 301 849 840 875 313 1188 .69 0 -.178 1.637 66 66 1.176 1.131 .85 .884 .715 98 12 62 67 431 436
17 620 617 1079 1971 1085 907 886 922 1131 2053 .86 0 .068 1.007 93 87 .994 .954 1.006 1.048 .922 170 32 62 68 455 461
18 467 451 922 1544 923 635 621 646 962 1608 .95 0 .061 .951 90 90 .999 .958 1.001 1.043 1.041 236 32 86 93 71 78
19 487 473 2754 3235 2632 623 603 628 2741 3369 .92 0 -.007 .968 100 96 1.046 1.005 .956 .995 .92 236 32 85 92 93 100
20 517 476 27 629 668 638 664 655 .26 -100 1.46 0 3 .404 560 80 85 95 117 127

Total number of rows: 4608

Table truncated, full table size 565 Kbytes.




Supplementary data files not provided

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