NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM499 Query DataSets for GSM499
Status Public on Jul 25, 2001
Title Tigr 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 Tigr 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 = hp3023
 
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 1139 1100 10775 13173 12706 492 467 381 10377 10758 0 0 -.054 1.106 86 94 .848 1.038 1.179 .963 0 1491 137 45 58 50 63 -.054
2 1182 1149 1677 4290 3802 517 488 399 3105 3504 1.89 0 .889 1.937 41 58 .441 .54 2.267 1.852 1.831 1463 137 45 58 74 87 .889
3 1217 1182 3644 5002 4484 552 518 423 3662 4085 0 0 .007 1.142 66 64 .813 .995 1.231 1.005 0 1463 137 45 58 98 111 .007
4 1214 1171 414 1104 582 536 522 426 475 902 .743 0 .199 .94 18 30 .711 .871 1.406 1.148 .937 1463 137 45 58 122 135 .199
5 1204 1163 169 700 182 521 518 423 149 572 .737 0 -.185 .871 13 22 .929 1.137 1.077 .88 .59 1463 137 45 58 146 159 -.185
6 1241 1176 4071 7646 7106 629 540 441 5803 6244 0 0 .512 1.602 67 69 .573 .701 1.746 1.426 0 1463 137 45 58 170 183 .512
7 1235 1192 504 1360 797 624 563 460 651 1111 .772 0 .369 1.481 22 37 .632 .774 1.581 1.291 1.198 1463 137 45 58 194 207 .369
8 1617 1248 607 966 365 714 601 491 298 789 .709 -100 .678 21 30 1.663 2.036 .601 .491 .319 1463 137 45 58 218 231 -1.026
9 1567 1205 1890 2949 2367 698 582 475 1933 2408 .728 0 .033 .978 53 66 .798 .978 1.252 1.023 .955 1463 137 45 58 242 255 .033
10 1176 1155 191 707 139 580 568 464 114 577 .724 0 -.751 .747 15 16 1.374 1.683 .728 .594 .573 1460 137 45 58 266 279 -.751
11 1264 1213 214 788 178 643 610 498 145 644 .784 0 -.558 .773 14 22 1.202 1.472 .832 .679 .623 1450 137 45 58 290 303 -.558
12 1402 1286 1439 5313 4669 717 644 526 3813 4339 3.982 0 1.406 3.122 51 64 .308 .377 3.245 2.65 2.811 1460 137 45 58 314 327 1.406
13 1435 1366 1039 1366 686 737 680 555 560 1116 .814 0 -.891 .582 51 59 1.515 1.855 .66 .539 .544 1463 137 45 58 338 351 -.891
14 1347 1321 1807 2749 2020 747 729 595 1650 2245 .898 0 -.131 1.116 47 61 .895 1.095 1.118 .913 1.036 1463 137 45 58 362 375 -.131
15 1333 1304 461 1281 546 761 735 600 446 1046 .746 0 -.048 1.021 23 27 .844 1.034 1.184 .967 .861 1463 137 45 58 386 399 -.048
16 1358 1313 338 1141 418 743 723 590 341 932 .811 0 .014 1.007 18 29 .809 .99 1.237 1.01 .875 1463 137 45 58 410 423 .014
17 1505 1471 625 1527 717 859 810 662 586 1247 .877 0 -.094 1.114 24 27 .872 1.067 1.147 .937 .961 1491 137 45 58 434 447 -.094
18 1190 1131 261 643 169 510 474 387 138 525 .718 0 -.919 .593 16 21 1.544 1.891 .648 .529 .445 1398 137 69 82 50 63 -.919
19 1203 1148 1205 1758 1274 519 484 395 1040 1436 .847 0 -.212 .919 35 46 .946 1.158 1.057 .863 .955 1372 137 69 82 74 87 -.212
20 1187 1154 52 544 41 533 503 411 33 444 .336 0 -.635 .648 1 12 1.268 1.553 .788 .644 .251 1421 137 69 82 98 111 -.635

Total number of rows: 4608

Table truncated, full table size 584 Kbytes.




Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap