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Sample GSM500 Query DataSets for GSM500
Status Public on Jul 25, 2001
Title 326 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 326 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 = hp3024
 
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
1 763 710 10062 12113 10591 1561 1522 1553 10807 12360 0 0 .103 .986 83 79 .95 .931 1.053 1.074 0 1491 137 35 48 51 64 .103
2 771 721 2100 3690 2111 1622 1579 1611 2154 3765 .819 0 .037 1.079 46 35 .995 .975 1.005 1.026 .814 1463 137 35 48 75 88 .037
3 779 735 3591 5629 3988 1685 1641 1674 4070 5744 0 0 .181 1.01 71 69 .9 .882 1.111 1.133 0 1463 137 35 48 99 112 .181
4 799 736 532 2261 617 1692 1644 1678 629 2307 .837 0 .242 1.324 27 20 .862 .846 1.16 1.182 1.028 1463 137 35 48 123 136 .242
5 783 710 88 1668 56 1663 1612 1645 57 1702 .5 0 -.627 1.02 11 3 1.571 1.544 .636 .648 .416 1488 137 35 48 147 160 -.627
6 782 717 4056 3772 2168 1631 1604 1637 2212 3849 0 0 -.875 .481 82 52 1.871 1.834 .535 .545 0 1462 137 35 48 174 187 -.875
7 790 721 634 2050 525 1568 1525 1556 536 2092 .733 0 -.242 1.141 23 16 1.208 1.183 .828 .845 .554 1441 137 35 48 196 209 -.242
8 823 721 169 1738 217 1595 1521 1552 221 1773 .683 0 .387 .922 14 11 .779 .765 1.284 1.308 .674 1463 137 35 48 220 233 .387
9 858 739 1539 3363 1802 1645 1561 1593 1839 3432 .79 0 .257 1.086 54 39 .854 .837 1.171 1.195 .928 1463 137 35 48 244 257 .257
10 775 723 111 1701 139 1597 1562 1594 142 1736 .534 0 .355 1.206 7 6 .799 .782 1.252 1.279 .543 1460 137 35 48 268 281 .355
11 764 719 185 1731 194 1559 1537 1568 198 1766 .692 0 .098 1.176 17 6 .954 .934 1.049 1.07 .617 1450 137 35 48 292 305 .098
12 768 729 2102 1676 167 1535 1509 1540 170 1710 .459 0 -3.628 .135 65 5 12.587 12.365 .079 .081 .051 1460 137 35 48 316 329 -3.628
13 818 738 960 1762 304 1528 1458 1488 310 1798 .605 0 -1.631 .536 37 15 3.158 3.097 .317 .323 .182 1463 137 35 48 340 353 -1.631
14 810 748 1239 3055 1606 1521 1449 1479 1638 3117 .774 0 .403 1.53 37 32 .771 .756 1.296 1.322 .88 1463 137 35 48 364 377 .403
15 797 742 381 1797 352 1506 1445 1474 360 1834 .553 0 -.082 1.265 26 13 1.082 1.058 .924 .945 .368 1463 137 35 48 388 401 -.082
16 826 753 291 1911 466 1522 1445 1474 476 1950 .598 0 .71 1.35 26 21 .624 .611 1.601 1.636 .544 1463 137 35 48 412 425 .71
17 819 769 390 1930 474 1524 1456 1486 483 1969 .621 0 .309 1.535 21 20 .823 .807 1.215 1.238 .538 1491 137 35 48 436 449 .309
18 768 711 116 1629 63 1615 1566 1598 64 1662 .18 0 -.858 .671 14 2 1.841 1.813 .543 .552 .132 1398 137 59 72 51 64 -.858
19 750 730 869 2478 856 1644 1622 1655 874 2529 .67 0 .008 1.054 27 23 1.015 .994 .985 1.006 .637 1355 137 59 72 75 88 .008
20 740 725 76 1626 1641 1630 1663 1659 .156 0 1.323 10 1 .108 1421 137 59 72 99 112

Total number of rows: 4608

Table truncated, full table size 581 Kbytes.




Supplementary data files not provided

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