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Sample GSM475 Query DataSets for GSM475
Status Public on Jul 25, 2001
Title 87A vs. TIGR/Astra ref. genomic DNA; amino-allyl labeling
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 87A genomic DNA
Organism Helicobacter pylori
Extracted molecule genomic DNA
 
 
Description Category: Strain comparison
Subcategory: Strain Comparison
Scanning Software: ScanAlyze
Software version: 2.42
Scanning parameters:
Lot batch = hp2039
 
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 (1)
GSE6 Genetic diversity among Helicobacter pylori strains

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
1 726 707 991 1022 992 914 -1 913 -.031 0 1.217 0 0 -.025 1462 112 52 64 39 51
2 849 790 3 1246 62 1262 1184 1091 57 1148 .243 0 4.251 1.051 3 0 .048 .053 20.667 19.038 .197 1337 112 51 63 58 70 4.251
3 956 898 3673 5580 4088 1512 1492 1374 3766 5140 0 0 .036 1.123 78 73 .898 .975 1.113 1.025 0 1326 268 49 66 75 95 .036
4 987 910 245 1418 14 1460 1404 1293 13 1306 .672 0 -4.248 .545 20 3 17.5 18.997 .057 .053 .496 1521 112 51 63 111 123 -4.248
5 1063 954 289 1462 23 1530 1439 1326 21 1347 .397 0 -3.77 .371 25 0 12.565 13.64 .08 .073 .152 1507 112 51 63 135 147 -3.77
6 1044 972 4047 3881 2346 1578 1535 1414 2161 3575 0 0 -.905 .639 74 59 1.725 1.873 .58 .534 0 1510 112 50 62 159 171 -.905
7 936 902 445 1772 305 1481 1467 1351 281 1632 .791 0 -.663 .676 34 10 1.459 1.584 .685 .631 .922 1509 112 50 62 183 195 -.663
8 919 872 257 1539 104 1448 1435 1322 96 1418 .584 0 -1.424 .554 23 3 2.471 2.683 .405 .373 .351 1509 112 50 62 207 219 -1.424
9 981 900 2740 4734 3302 1474 1432 1319 3042 4361 .875 0 .151 1.174 66 68 .83 .901 1.205 1.11 .947 1495 112 50 62 231 243 .151
10 977 896 310 1548 171 1414 1377 1268 158 1426 .703 0 -.977 .825 29 14 1.813 1.968 .552 .508 .512 1456 112 49 61 255 267 -.977
11 994 950 467 1758 315 1470 1443 1329 290 1619 .645 0 -.687 .729 28 20 1.483 1.609 .675 .621 .427 1483 112 49 61 279 291 -.687
12 1074 1031 2178 1569 14 1578 1555 1432 13 1445 .423 0 -7.4 .113 59 1 155.571 168.881 .006 .006 .066 1511 112 49 61 303 315 -7.4
13 1071 1033 2080 2352 826 1552 1526 1406 761 2167 .723 0 -1.451 .442 74 50 2.518 2.734 .397 .366 .309 1518 112 49 61 327 339 -1.451
14 1070 1014 3364 4917 3360 1592 1557 1434 3095 4529 .865 0 -.12 1.002 81 74 1.001 1.087 .999 .92 .821 1518 112 48 60 352 364 -.12
15 1004 968 196 1640 68 1590 1572 1448 63 1511 .619 0 -1.646 .496 25 3 2.882 3.129 .347 .32 .24 1509 112 48 60 376 388 -1.646
16 995 940 1232 2721 1262 1497 1459 1344 1163 2507 .877 0 -.084 1.036 50 50 .976 1.06 1.024 .944 .838 1509 112 48 60 400 412 -.084
17 899 851 2423 4113 2909 1237 1204 1109 2680 3789 .85 0 .145 1.161 65 62 .833 .904 1.201 1.106 .998 1534 112 48 60 424 436 .145
18 832 781 551 1714 535 1222 1179 1086 493 1579 .818 0 -.161 1.243 38 26 1.03 1.118 .971 .894 .716 1504 112 76 88 39 51 -.161
19 1049 991 3191 3963 2351 1604 1612 1485 2166 3651 .813 0 -.559 .72 94 61 1.357 1.473 .737 .679 .66 1441 112 75 87 63 75 -.559
20 1104 1050 303 1662 1700 1683 1550 -19 1531 .724 0 .571 19 4 .487 1439 112 75 87 87 99

Total number of rows: 4608

Table truncated, full table size 559 Kbytes.




Supplementary data files not provided
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