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Sample GSM470 Query DataSets for GSM470
Status Public on Jul 25, 2001
Title Tigr wizard prep vs. astr/tigr ref genomic DNA
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 Tigr Genomic DNA (wizard prep)
Organism Helicobacter pylori
Extracted molecule genomic DNA
 
 
Description Category: Genomic DNA
Subcategory: Strain Comparison
Scanning Software: ScanAlyze
Software version: 2.33
Scanning parameters:
Lot batch = hp2027
 
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 (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 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 2619 542 258 9205 285 206 -20 187 -.034 0 1.524 0 0 -.018 1522 112 64 76 29 41
2 2236 554 253 6985 308 223 -40 183 .078 0 0 0 0 .036 1509 112 64 76 53 65
3 1324 562 246 3896 326 236 -58 178 .03 0 0 0 0 .019 1511 112 64 76 77 89
4 751 584 156 533 146 1632 387 280 106 386 .73 0 -.561 .846 20 23 1.068 1.476 .936 .678 .77 1522 112 63 75 101 113 -.561
5 610 601 155 543 134 438 409 296 97 393 .735 0 -.676 .855 24 27 1.157 1.598 .865 .626 .936 1521 112 63 75 125 137 -.676
6 636 632 2085 4788 4329 467 459 332 3134 3467 0 0 .588 1.828 69 75 .482 .665 2.076 1.503 0 1517 112 63 75 150 162 .588
7 649 642 260 702 239 463 463 335 173 508 .553 0 -.587 .817 24 25 1.088 1.503 .919 .666 .65 1509 112 63 75 174 186 -.587
8 640 632 136 626 172 452 454 329 125 453 .664 0 -.127 .991 18 24 .791 1.092 1.265 .916 .93 1509 112 63 75 198 210 -.127
9 630 623 1073 2211 1759 449 452 327 1274 1601 .807 0 .247 1.492 69 75 .61 .843 1.639 1.187 1.307 1509 112 63 75 222 234 .247
10 635 630 98 560 115 443 445 322 83 405 .639 0 -.235 .867 19 21 .852 1.177 1.173 .85 .821 1520 112 62 74 246 258 -.235
11 626 621 204 636 207 430 429 311 150 460 .707 0 -.445 .9 23 26 .986 1.361 1.015 .735 .83 1510 112 62 74 270 282 -.445
12 590 588 1058 4469 4093 389 376 272 2963 3236 .864 0 1.486 4.317 75 93 .258 .357 3.869 2.801 3.053 1511 112 62 74 294 306 1.486
13 635 573 1454 954 597 402 357 258 432 691 .695 0 -1.75 .362 76 57 2.436 3.364 .411 .297 .38 1521 112 62 74 318 330 -1.75
14 662 589 1645 2526 2128 458 398 288 1541 1829 .891 0 -.094 1.22 69 69 .773 1.068 1.294 .937 1.116 1517 112 62 74 343 355 -.094
15 646 572 400 992 616 440 376 272 446 718 .878 0 .157 1.558 51 84 .649 .897 1.54 1.115 1.17 1509 112 62 74 367 379 .157
16 574 570 657 1154 783 370 371 269 567 836 .869 0 -.213 1.202 50 58 .839 1.159 1.192 .863 .923 1520 112 61 73 391 403 -.213
17 558 556 987 1278 934 351 344 249 676 925 .814 0 -.546 1.013 58 66 1.057 1.46 .946 .685 .764 1535 112 61 73 415 427 -.546
18 537 529 420 861 582 287 279 202 421 623 .795 0 .005 1.573 54 80 .722 .997 1.386 1.003 .881 1509 112 88 100 29 41 .005
19 567 562 1537 2504 2177 327 327 237 1576 1813 .854 0 .036 1.461 73 75 .706 .975 1.416 1.026 1.239 1498 112 88 100 53 65 .036
20 579 575 270 514 159 350 355 257 115 372 .792 0 -1.23 .704 22 29 1.698 2.345 .589 .426 .564 1509 112 88 100 77 89 -1.23

Total number of rows: 4608

Table truncated, full table size 559 Kbytes.




Supplementary data files not provided

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