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Sample GSM503 Query DataSets for GSM503
Status Public on Jul 25, 2001
Title 314 vs. Tigr/Astra ref trial 3
Sample type genomic
 
Channel 1
Source name 0.7 ug Astra genomic DNA +0.7 ug Tigr genomic DNA
Organism Helicobacter pylori
Extracted molecule genomic DNA
 
Channel 2
Source name 2ug 314 genomic DNA
Organism Helicobacter pylori
Extracted molecule genomic DNA
 
 
Description Category: Genomic DNA
Subcategory: Strain Comparison
2ug T2 genomic DNA vs. 0.7 ug Astra genomic DNA +0.7 ug Tigr genomic DNA
Scanning Software: GenePix
Software version: Pro
Scanning parameters:
Lot batch = hp4069
 
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
1 436 427 10996 6862 6512 368 350 538 10018 10556 .98 0 -.134 .543 100 100 1.689 1.098 .592 .911 .599 306 52 54 62 66 74
2 491 477 6240 1130 770 373 360 553 1185 1738 .86 0 -2.397 .128 100 78 8.104 5.266 .123 .19 .124 236 32 53 60 91 98
3 429 430 2832 1839 1494 366 345 530 2299 2829 .94 0 -.301 .542 94 86 1.896 1.232 .528 .812 .5 332 52 53 61 115 123
4 434 423 30 367 31 370 336 516 48 564 -100 .678 1.519 22 13 .968 .625 1.033 1.6 552 80 52 62 139 149
5 447 445 371 6 381 365 561 9 570 .04 -100 1.222 16 17 .066 538 80 51 61 163 173
6 497 478 2031 881 523 376 358 550 805 1355 .81 0 -1.335 .226 100 69 3.883 2.523 .258 .396 .25 309 52 51 59 188 196
7 466 459 243 429 57 387 372 572 88 660 .22 0 -1.465 .732 76 25 4.263 2.761 .235 .362 .218 332 52 52 60 212 220
8 446 447 1355 967 586 388 381 586 901 1487 .8 0 -.589 .563 100 83 2.312 1.504 .432 .665 .407 90 12 52 57 236 241
9 479 465 3216 2656 2293 397 363 558 3528 4086 .94 0 .134 .655 98 90 1.403 .912 .713 1.097 .701 405 52 50 59 259 268
10 487 474 180 477 92 402 385 592 141 733 .41 -100 -.352 .826 43 31 1.957 1.277 .511 .783 .328 552 80 51 61 283 293
11 494 484 205 569 187 406 382 587 288 875 .7 -100 .49 .992 41 43 1.096 .712 .912 1.405 .558 552 80 51 61 307 317
12 563 550 6856 737 350 405 387 595 538 1133 .64 0 -3.672 .046 100 65 19.589 12.743 .051 .078 .048 230 32 51 58 333 340
13 520 508 1472 1471 1060 431 411 632 1631 2263 .83 0 .148 .731 94 92 1.389 .903 .72 1.108 .603 332 52 51 59 356 364
14 555 560 2458 1922 1528 424 394 606 2350 2956 .89 0 -.065 .655 96 96 1.609 1.046 .622 .956 .504 230 32 51 58 380 387
15 534 528 1898 1676 1257 437 419 644 1934 2578 .92 0 .027 .609 91 91 1.51 .981 .662 1.019 .648 90 12 51 56 404 409
16 586 577 596 777 339 454 438 673 522 1195 .63 0 -.191 .746 75 75 1.758 1.142 .569 .876 .462 104 12 53 58 430 435
17 566 554 1122 1065 640 443 425 653 985 1638 .77 0 -.188 .585 96 87 1.753 1.139 .57 .878 .477 220 32 50 57 452 459
18 433 430 1143 641 290 375 351 540 446 986 .67 0 -1.358 .262 93 56 3.941 2.563 .254 .39 .204 176 32 78 84 70 76
19 453 445 2358 1744 1379 385 365 561 2122 2683 .91 0 -.152 .538 98 98 1.71 1.111 .585 .9 .574 340 52 76 84 93 101
20 461 452 59 408 30 384 378 581 46 627 .03 -100 -.359 1.256 35 20 1.967 1.283 .508 .78 .052 560 80 76 86 115 125

Total number of rows: 4608

Table truncated, full table size 563 Kbytes.




Supplementary data files not provided
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