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Sample GSM489 Query DataSets for GSM489
Status Public on Jul 25, 2001
Title Hp1 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 Hp1 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 = hp3004
 
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
1 348 339 3019 4163 4016 158 147 140 3831 3971 .739 0 .344 1.366 66 83 .752 .788 1.33 1.269 .999 1525 112 58 70 50 62 .344
2 352 340 1576 1634 1485 161 149 142 1417 1559 .572 0 -.154 .812 61 70 1.061 1.113 .942 .899 .549 1505 112 58 70 74 86 -.154
3 370 344 2749 3503 3343 175 160 153 3189 3341 .541 0 .214 1.252 95 99 .822 .862 1.216 1.16 .588 1505 112 58 70 98 110 .214
4 366 343 909 1155 991 177 164 156 945 1102 .645 0 .057 .89 68 79 .917 .962 1.09 1.04 .693 1505 112 58 70 122 134 .057
5 345 336 152 311 148 172 163 155 141 297 .439 0 -.107 .565 19 35 1.027 1.077 .974 .929 .381 1505 112 58 70 146 158 -.107
6 347 339 1098 860 691 178 169 161 659 820 .546 0 -.736 .592 50 58 1.589 1.666 .629 .6 .325 1527 112 58 70 170 182 -.736
7 404 383 432 578 370 217 208 198 353 551 .603 0 -.292 .706 46 52 1.168 1.224 .856 .817 .519 1521 112 58 70 197 209 -.292
8 523 512 141 348 77 283 271 259 73 332 .466 0 -.941 .581 16 16 1.831 1.92 .546 .521 .22 1509 112 58 70 221 233 -.941
9 605 588 814 1331 1001 346 330 315 955 1270 .584 0 .23 1.109 48 55 .813 .852 1.23 1.173 .702 1495 112 58 70 245 257 .23
10 652 634 164 586 201 406 385 367 192 559 .349 0 .225 1.279 15 30 .816 .855 1.226 1.169 .353 1428 112 58 70 269 281 .225
11 715 694 227 620 161 476 459 438 154 591 .392 0 -.564 .816 19 23 1.41 1.478 .709 .677 .322 1411 112 58 70 293 305 -.564
12 812 782 1269 896 338 569 558 532 322 855 .476 0 -1.977 .264 82 60 3.754 3.936 .266 .254 .14 1485 112 58 70 317 329 -1.977
13 874 840 1111 1637 1003 647 634 605 957 1562 .32 0 -.216 .85 74 83 1.108 1.161 .903 .861 .266 1509 112 58 70 341 353 -.216
14 869 854 753 1378 721 664 657 627 688 1314 .555 0 -.131 .878 35 40 1.044 1.095 .958 .913 .496 1509 112 58 70 365 377 -.131
15 876 833 467 911 267 671 644 614 255 869 .236 0 -.875 .811 39 33 1.749 1.834 .572 .545 .151 1506 112 58 70 389 401 -.875
16 823 747 86 633 79 606 554 528 75 604 .252 0 -.191 .825 9 13 1.089 1.141 .919 .876 .202 1490 112 58 70 413 425 -.191
17 752 719 176 702 181 542 521 497 173 670 .492 0 -.028 1.013 17 23 .972 1.019 1.028 .981 .484 1513 112 58 70 437 449 -.028
18 403 386 317 383 184 211 199 190 176 365 .292 0 -.853 .7 51 52 1.723 1.806 .58 .554 .161 1485 112 82 94 53 65 -.853
19 401 382 196 463 273 208 190 181 260 442 .782 0 .41 1.089 25 34 .718 .753 1.393 1.329 1.08 1470 112 82 94 77 89 .41
20 413 371 13 184 231 188 179 -4 176 .37 0 .535 8 8 .239 1483 112 82 94 101 113

Total number of rows: 4608

Table truncated, full table size 573 Kbytes.




Supplementary data files not provided

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