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Sample GSM505 Query DataSets for GSM505
Status Public on Jul 25, 2001
Title Astra genomic DNA vs TIGR/Astra reference, trial 2
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, trial 2
Scanning Software: GenePix
Software version: Pro
Scanning parameters:
Lot batch = hp4068
 
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
1 442 436 11377 8419 7970 472 449 488 8663 9151 .96 0 -.393 .672 100 100 1.427 1.313 .701 .761 .687 206 32 42 49 57 64
2 433 425 4069 1129 675 484 454 493 734 1227 .79 0 -2.471 .187 100 63 6.028 5.544 .166 .18 .156 340 52 41 49 81 89
3 449 437 4215 3840 3394 477 446 484 3689 4173 .94 0 -.192 .691 100 96 1.242 1.143 .805 .875 .816 230 32 40 47 106 113
4 453 446 41 501 37 484 464 504 40 544 .18 -100 -.036 1.773 27 18 1.108 1.025 .902 .976 .391 552 80 39 49 130 140
5 469 465 58 496 26 497 470 510 29 539 .09 -100 -1 1.402 26 17 2.231 2 .448 .5 .192 552 80 39 49 154 164
6 514 509 3200 1380 882 508 498 541 959 1500 .92 0 -1.738 .287 100 84 3.628 3.337 .276 .3 .281 170 32 41 47 180 186
7 509 506 123 649 147 522 502 545 160 705 .64 -100 .379 1.278 38 23 .837 .769 1.195 1.301 1.057 552 80 39 49 202 212
8 510 502 551 833 312 554 521 566 339 905 .58 0 -.701 .649 91 57 1.766 1.625 .566 .615 .481 98 12 41 46 228 233
9 558 549 2584 2299 1758 559 541 588 1910 2498 .95 0 -.436 .66 98 90 1.47 1.353 .68 .739 .639 320 52 39 47 251 259
10 578 570 90 604 38 594 566 615 41 656 .12 -100 -1.134 1.49 37 16 2.368 2.195 .422 .456 .224 552 80 39 49 274 284
11 597 587 138 680 128 586 552 600 139 739 .31 -100 .01 1.194 40 31 1.078 .993 .928 1.007 .458 552 80 39 49 298 308
12 628 619 6746 864 308 591 556 604 335 939 .53 0 -4.332 .066 100 56 21.903 20.137 .046 .05 .04 420 52 39 48 323 332
13 620 625 2567 3272 2664 606 608 660 2896 3556 .95 0 .174 1.019 100 100 .964 .886 1.038 1.128 .985 170 32 41 47 349 355
14 661 659 3421 3180 2570 632 610 663 2793 3456 .96 0 -.293 .712 100 96 1.331 1.225 .751 .816 .731 236 32 40 47 372 379
15 644 635 2536 1722 1099 635 623 677 1194 1871 .88 0 -1.087 .466 96 87 2.308 2.124 .433 .471 .378 230 32 39 46 396 403
16 671 664 643 1177 597 618 580 630 649 1279 .82 0 .013 .97 84 75 1.077 .991 .928 1.009 .782 170 32 41 47 421 427
17 685 671 1723 2501 1777 713 724 786 1932 2718 .93 0 .165 .932 100 96 .97 .892 1.031 1.121 1.053 160 32 40 46 445 451
18 425 422 1562 1626 1212 448 414 450 1317 1767 .87 0 -.246 .719 100 78 1.289 1.186 .776 .843 .679 176 32 65 71 61 67
19 446 440 2393 2533 2079 461 454 493 2260 2753 .89 0 -.082 .898 100 100 1.151 1.059 .869 .944 .792 176 32 65 71 85 91
20 461 452 57 510 61 468 449 488 66 554 .12 -100 .212 2.088 33 25 .934 .864 1.07 1.158 .229 560 80 63 73 106 116

Total number of rows: 4608

Table truncated, full table size 572 Kbytes.




Supplementary data files not provided

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