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Sample GSM487 Query DataSets for GSM487
Status Public on Jul 25, 2001
Title G50 genomic DNA vs. Tigr/Astra reference
Sample type genomic
 
Channel 1
Source name 1 ug Tigr genomic DNA, 1 ug Astra genomic DNA
Organism Helicobacter pylori
Extracted molecule genomic DNA
 
Channel 2
Source name 2 ug G50 genomic DNA
Organism Helicobacter pylori
Extracted molecule genomic DNA
 
 
Description Category: Genomic DNA
Subcategory: Strain Comparison
Scanning Software: ScanAlyze
Software version: 2.42
Scanning parameters:
Lot batch = hp3002
 
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
1 331 282 2391 1991 1759 258 232 374 2837 3211 .83 0 .247 .796 48 49 1.359 .843 .736 1.187 .63 1453 156 53 67 57 71 .247
2 322 292 2020 1287 1052 251 235 379 1697 2076 .793 0 -.251 .513 59 51 1.92 1.19 .521 .84 .42 1415 156 53 67 81 95 -.251
3 347 318 2561 2022 1769 271 253 408 2853 3261 .788 0 .156 .692 76 75 1.448 .898 .691 1.114 .546 1415 156 53 67 105 119 .156
4 358 331 885 813 548 282 265 427 884 1311 .677 0 -.002 .586 57 46 1.615 1.001 .619 .999 .449 1414 156 53 67 129 143 -.002
5 379 351 222 410 131 295 279 450 211 661 .549 0 -.073 .624 25 22 1.695 1.052 .59 .95 .388 1414 156 53 67 153 167 -.073
6 388 357 848 623 341 297 282 455 550 1005 .687 0 -.625 .433 46 33 2.487 1.542 .402 .649 .289 1440 156 53 67 177 191 -.625
7 390 350 666 615 346 291 269 434 558 992 .673 0 -.255 .406 45 36 1.925 1.194 .52 .838 .375 1438 156 53 67 203 217 -.255
8 427 380 202 387 109 303 278 448 176 624 .718 0 -.199 .447 26 20 1.853 1.148 .54 .871 .508 1416 156 53 67 227 241 -.199
9 474 449 973 1109 791 332 318 513 1276 1789 .678 0 .391 .688 49 50 1.23 .763 .813 1.311 .539 1402 156 53 67 251 265 .391
10 538 505 283 572 224 361 348 561 362 923 .64 0 .355 .67 19 17 1.263 .782 .792 1.279 .509 1420 156 52 66 275 289 .355
11 578 542 211 564 202 374 362 584 326 910 .447 0 .628 .576 16 21 1.045 .647 .957 1.545 .371 1420 156 52 66 299 313 .628
12 613 584 1407 552 175 387 377 608 282 890 .59 0 -2.319 .18 65 41 8.04 4.989 .124 .2 .11 1420 156 52 66 323 337 -2.319
13 694 674 588 880 457 433 423 682 737 1419 .418 0 .326 .699 44 53 1.287 .798 .777 1.253 .325 1420 156 52 66 347 361 .326
14 822 798 585 915 410 514 505 815 661 1476 .74 0 .176 .637 34 33 1.427 .885 .701 1.13 .502 1420 156 52 66 371 385 .176
15 857 843 42 625 102 529 523 844 164 1008 .464 0 1.965 .71 16 25 .412 .256 2.429 3.905 .354 1420 156 52 66 395 409 1.965
16 838 810 42 537 43 509 494 797 69 866 .36 0 .716 1 8 11 .977 .609 1.024 1.643 .243 1420 156 52 66 419 433 .716
17 864 804 58 508 36 496 472 761 58 819 .532 0 0 .606 8 10 1.611 1 .621 1 .343 1462 156 52 66 443 457 0
18 344 291 175 342 103 261 239 385 167 552 .588 0 -.068 .795 35 31 1.699 1.048 .589 .954 .326 1411 156 77 91 60 74 -.068
19 342 309 260 426 180 263 246 397 290 687 .695 0 .158 .692 31 28 1.444 .897 .692 1.115 .485 1384 156 77 91 84 98 .158
20 362 329 55 290 30 276 260 419 49 468 .48 0 -.167 .685 16 10 1.833 1.122 .545 .891 .336 1384 156 77 91 108 122 -.167

Total number of rows: 4608

Table truncated, full table size 561 Kbytes.




Supplementary data files not provided

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