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Sample GSM493 Query DataSets for GSM493
Status Public on Jul 25, 2001
Title G39 genomic DNA vs. Tigr/Astra reference DNA
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 G39 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 = hp3007
 
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
1 265 261 2439 2726 2630 97 96 107 2922 3029 .764 0 .261 1.011 75 86 .927 .835 1.078 1.198 .798 1525 112 45 57 54 66 .261
2 275 270 999 595 492 105 103 114 547 661 .686 0 -.869 .425 56 54 2.03 1.826 .492 .548 .342 1508 112 45 57 78 90 -.869
3 311 278 1301 1318 1207 141 111 123 1341 1464 .735 0 .044 .897 62 67 1.078 .97 .928 1.031 .665 1508 112 45 57 102 114 .044
4 581 284 692 751 633 252 118 131 703 834 .582 0 .023 .711 58 69 1.093 .984 .915 1.016 .511 1508 112 45 57 126 138 .023
5 293 286 98 176 54 125 122 136 60 196 .485 0 -.708 .512 21 22 1.815 1.633 .551 .612 .257 1508 112 45 57 150 162 -.708
6 308 297 777 461 333 131 128 142 370 512 .748 0 -1.07 .371 48 50 2.333 2.1 .429 .476 .32 1526 112 45 57 174 186 -1.07
7 308 300 170 266 133 136 133 148 148 296 .743 0 -.2 .572 28 34 1.278 1.149 .782 .871 .492 1521 112 45 57 200 212 -.2
8 316 309 69 183 39 149 144 160 43 203 .789 0 -.682 .608 14 15 1.769 1.605 .565 .623 .472 1509 112 45 57 224 236 -.682
9 320 316 382 591 436 157 155 172 485 657 .697 0 .344 1.019 47 58 .876 .788 1.141 1.27 .761 1488 112 45 57 248 260 .344
10 324 320 115 249 84 166 165 183 94 277 .704 0 -.291 .608 18 18 1.369 1.223 .73 .817 .563 1448 112 45 57 272 284 -.291
11 334 325 76 223 55 175 168 187 61 248 .615 0 -.317 .75 13 15 1.382 1.246 .724 .803 .39 1441 112 45 57 296 308 -.317
12 374 339 1339 1627 1449 196 178 198 1610 1808 .634 0 .266 1.032 84 95 .924 .832 1.082 1.202 .56 1490 112 45 57 320 332 .266
13 388 346 517 669 490 198 179 199 544 743 .59 0 .073 .844 62 68 1.055 .95 .948 1.052 .576 1509 112 45 57 344 356 .073
14 359 343 322 480 318 169 162 180 353 533 .695 0 .133 .921 34 42 1.013 .912 .988 1.096 .669 1509 112 45 57 368 380 .133
15 364 343 159 300 125 188 175 194 139 333 .632 0 -.194 .569 24 30 1.272 1.144 .786 .874 .377 1506 112 45 57 392 404 -.194
16 366 336 45 238 46 214 192 213 51 264 .468 0 .181 .655 12 18 .978 .882 1.022 1.133 .43 1490 112 45 57 416 428 .181
17 367 335 101 288 89 210 199 221 99 320 .662 0 -.029 .621 21 23 1.135 1.02 .881 .98 .515 1513 112 45 57 440 452 -.029
18 286 274 291 280 177 109 103 114 197 311 .603 0 -.563 .619 57 65 1.644 1.477 .608 .677 .324 1487 112 69 81 56 68 -.563
19 286 276 155 232 121 113 111 123 135 258 .725 0 -.199 .569 25 32 1.281 1.148 .781 .871 .486 1472 112 69 81 80 92 -.199
20 405 282 17 119 3 202 116 129 3 132 .206 0 -2.502 .655 5 6 5.667 5.667 .176 .176 .094 1485 112 69 81 104 116 -2.502

Total number of rows: 4608

Table truncated, full table size 569 Kbytes.




Supplementary data files not provided
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