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Sample GSM492 Query DataSets for GSM492
Status Public on Jul 25, 2001
Title 87A 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 87A 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 = hp3008
 
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
1 482 478 1790 3721 3639 88 82 65 2883 2948 .837 0 .688 2 77 85 .492 .621 2.033 1.611 1.776 1522 112 41 53 40 52 .688
2 485 482 647 1049 967 83 82 65 766 831 .82 0 .244 1.216 52 67 .669 .845 1.495 1.184 1.2 1509 112 41 53 64 76 .244
3 490 486 927 1642 1560 87 82 65 1236 1301 .82 0 .415 1.538 65 79 .594 .75 1.683 1.333 1.319 1509 112 41 53 88 100 .415
4 488 480 621 913 831 87 82 65 658 723 .631 0 .084 1.144 66 87 .747 .943 1.338 1.06 .949 1509 112 41 53 112 124 .084
5 498 490 89 195 110 86 85 67 87 154 .791 0 -.03 .904 15 30 .809 1.021 1.236 .979 .813 1509 112 41 53 136 148 -.03
6 511 502 920 533 441 93 92 73 349 422 .874 0 -1.397 .444 65 76 2.086 2.633 .479 .38 .435 1509 112 41 53 160 172 -1.397
7 494 490 160 255 158 99 97 77 125 202 .703 0 -.354 .724 17 38 1.013 1.278 .988 .782 .621 1509 112 41 53 184 196 -.354
8 491 485 94 166 64 105 102 81 51 132 .709 0 -.891 .536 13 29 1.469 1.854 .681 .539 .552 1509 112 41 53 208 220 -.891
9 494 491 370 768 659 114 109 86 522 608 .755 0 .497 1.644 41 61 .561 .709 1.781 1.411 1.286 1499 112 41 53 232 244 .497
10 514 507 94 246 127 128 119 94 101 195 .712 0 .098 .902 11 39 .74 .934 1.351 1.07 .808 1427 112 42 54 256 268 .098
11 534 519 62 202 68 142 134 106 54 160 .602 0 -.203 .734 11 25 .912 1.151 1.097 .869 .65 1397 112 42 54 280 292 -.203
12 613 570 1341 330 185 157 145 115 147 261 .729 0 -3.194 .144 89 82 7.249 9.149 .138 .109 .103 1396 112 42 54 304 316 -3.194
13 673 644 597 359 190 181 169 134 151 284 .588 0 -1.988 .389 53 58 3.142 3.966 .318 .252 .216 1418 112 42 54 327 339 -1.988
14 617 587 256 662 472 196 190 151 374 524 .779 0 .547 1.725 25 39 .542 .685 1.844 1.461 1.442 1493 112 42 54 351 363 .547
15 555 543 163 267 77 203 190 151 61 212 .775 0 -1.418 .606 22 19 2.117 2.672 .472 .374 .476 1506 112 42 54 375 387 -1.418
16 571 543 36 266 67 233 199 158 53 211 .568 0 .56 .986 5 22 .537 .678 1.861 1.475 .695 1490 112 42 54 399 411 .56
17 594 550 125 357 144 263 213 169 114 283 .748 0 -.132 .846 15 25 .868 1.096 1.152 .913 .832 1513 112 42 54 423 435 -.132
18 533 512 340 287 198 113 89 71 157 227 .655 0 -1.116 .592 46 72 1.717 2.167 .582 .461 .262 1490 112 65 77 40 52 -1.116
19 530 500 110 292 202 97 90 71 160 231 .806 0 .541 1.21 22 41 .545 .687 1.836 1.455 1.267 1475 112 65 77 64 76 .541
20 490 480 15 103 12 96 91 72 10 82 .537 0 -.658 .569 1 14 1.25 1.578 .8 .634 .313 1488 112 65 77 88 100 -.658

Total number of rows: 4608

Table truncated, full table size 558 Kbytes.




Supplementary data files not provided

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