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Sample GSM484 Query DataSets for GSM484
Status Public on Jul 25, 2001
Title CCUG genomic DNA vs Tigr/Astra reference
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 2ug CCUG 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 = hp2031
 
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
1 565 542 1498 1102 338 785 764 2938 1300 4238 .659 0 -.205 .415 41 27 4.432 1.152 .226 .868 .179 1478 112 33 45 43 55 -.205
2 571 560 375 853 71 792 782 3008 273 3281 .181 0 -.458 .798 35 5 5.282 1.374 .189 .728 .06 1452 112 33 45 63 75 -.458
3 584 576 3545 1560 781 795 779 2996 3004 6000 .656 0 -.239 .213 72 67 4.539 1.18 .22 .847 .152 1532 137 30 43 87 100 -.239
4 567 564 51 795 12 793 783 3012 46 3058 .019 0 -.149 1.307 8 4 4.25 1.109 .235 .902 .024 1522 112 32 44 116 128 -.149
5 570 562 64 788 7 800 781 3004 27 3031 .171 0 -1.245 1.904 10 3 9.143 2.37 .109 .422 .173 1493 112 32 44 140 152 -1.245
6 576 560 1494 1038 262 795 776 2985 1007 3992 .553 0 -.569 .237 68 30 5.702 1.484 .175 .674 .125 1470 177 28 43 163 178 -.569
7 605 587 183 852 64 807 788 3031 246 3277 .406 0 .427 .759 18 10 2.859 .744 .35 1.344 .279 1484 112 31 43 188 200 .427
8 606 588 179 821 31 809 790 3038 120 3158 .089 0 -.577 .69 21 6 5.774 1.492 .173 .67 .107 1507 112 31 43 212 224 -.577
9 565 558 1045 946 202 766 744 2862 776 3638 .618 0 -.429 .254 58 26 5.173 1.347 .193 .743 .159 1505 112 30 42 236 248 -.429
10 576 564 147 775 33 759 742 2854 127 2981 .258 0 -.211 .996 16 8 4.455 1.157 .224 .864 .238 1463 112 30 42 260 272 -.211
11 617 598 236 851 64 801 787 3027 246 3273 .048 0 .06 1.028 21 8 3.688 .959 .271 1.042 .025 1447 112 30 42 284 296 .06
12 634 611 797 782 11 786 771 2965 43 3008 -.005 0 -4.212 .231 58 5 72.455 18.535 .014 .054 -.001 1463 177 28 43 307 322 -4.212
13 608 598 557 776 43 757 733 2819 166 2985 .183 0 -1.746 .426 44 11 12.953 3.355 .077 .298 .05 1450 177 26 41 334 349 -1.746
14 635 624 1388 1217 478 762 739 2842 1839 4681 .61 0 .406 .409 66 51 2.904 .755 .344 1.325 .234 1453 112 29 41 357 369 .406
15 626 616 227 776 57 743 719 2765 220 2985 -.085 0 -.045 .974 28 9 3.982 1.032 .251 .969 -.079 1510 112 28 40 381 393 -.045
16 633 624 776 951 237 729 714 2746 912 3658 .471 0 .233 .319 58 25 3.274 .851 .305 1.175 .19 1509 112 28 40 405 417 .233
17 625 610 1314 1060 353 728 707 2719 1358 4077 .654 0 .048 .364 57 33 3.722 .968 .269 1.033 .165 1534 112 28 40 429 441 .048
18 553 543 306 796 44 768 752 2892 170 3062 .289 0 -.848 .879 32 8 6.955 1.8 .144 .556 .123 1500 112 57 69 44 56 -.848
19 574 564 1283 1161 389 786 772 2969 1496 4465 .55 0 .222 .351 63 42 3.298 .858 .303 1.166 .188 1497 112 57 69 68 80 .222
20 574 570 176 785 20 780 765 2942 77 3019 .265 0 -1.193 .672 16 7 8.8 2.286 .114 .438 .185 1501 112 57 69 92 104 -1.193

Total number of rows: 4608

Table truncated, full table size 566 Kbytes.




Supplementary data files not provided

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