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Sample GSM485 Query DataSets for GSM485
Status Public on Jul 25, 2001
Title G39 genomic DNA vs. Tigr/Astra reference
Sample type genomic
 
Channel 1
Source name 1ug Tigr genomic DNA, 1 ug 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 = hp2051
 
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
1 547 356 6 171 9 197 162 95 5 101 .091 0 -.178 .947 0 5 .667 1.131 1.5 .884 .108 1447 156 38 52 30 44 -.178
2 547 355 181 221 181 107 0 107 -.06 0 1.333 0 5 -.068 1453 156 38 52 54 68
3 373 356 2139 4471 4286 231 185 109 2526 2635 0 0 .24 1.878 78 88 .499 .847 2.004 1.181 0 1425 156 38 52 81 95 .24
4 368 358 58 274 86 200 188 111 51 161 .518 0 -.195 1.371 13 30 .674 1.144 1.483 .874 .553 1396 156 39 53 103 117 -.195
5 369 363 106 321 137 191 184 108 81 189 .718 0 -.393 1.597 17 36 .774 1.313 1.292 .762 .901 1422 156 39 53 127 141 -.393
6 390 371 1164 1152 965 206 187 110 569 679 .529 0 -1.033 .792 64 66 1.206 2.047 .829 .489 .416 1420 156 39 53 151 165 -1.033
7 378 364 121 386 197 200 189 111 116 227 .709 0 -.06 1.301 24 44 .614 1.042 1.628 .959 1.055 1420 156 39 53 175 189 -.06
8 364 355 45 242 53 200 189 111 31 143 .477 0 -.527 1.209 9 21 .849 1.441 1.178 .694 .45 1420 156 39 53 199 213 -.527
9 361 350 687 1434 1242 204 192 113 732 845 .641 0 .091 1.983 65 82 .553 .939 1.808 1.065 1.089 1432 156 39 53 223 237 .091
10 363 354 113 367 175 202 192 113 103 216 .625 0 -.132 1.355 29 37 .646 1.096 1.549 .913 .862 1432 156 39 53 248 262 -.132
11 374 368 157 459 253 219 206 121 149 270 .762 0 -.075 1.263 32 43 .621 1.053 1.611 .95 1.067 1425 156 39 53 272 286 -.075
12 380 372 741 2191 1962 244 229 135 1156 1291 .492 0 .642 2.541 53 75 .378 .641 2.648 1.56 1.092 1435 156 39 53 296 310 .642
13 378 368 512 1109 879 242 230 136 518 654 .745 0 .017 1.838 54 80 .582 .988 1.717 1.012 1.193 1450 156 40 54 320 334 .017
14 380 371 952 2177 1943 244 234 138 1145 1283 .718 0 .266 1.9 70 83 .49 .831 2.041 1.203 1.438 1393 156 40 54 347 361 .266
15 377 366 132 465 237 238 228 134 140 274 .195 0 .081 2.092 23 42 .557 .945 1.795 1.058 .234 1392 156 40 54 368 382 .081
16 377 370 381 1015 782 242 233 137 461 598 .8 0 .274 1.956 35 46 .487 .827 2.052 1.21 1.671 1428 156 40 54 393 407 .274
17 377 373 743 1648 1417 239 231 136 835 971 .613 0 .169 1.847 40 67 .524 .89 1.907 1.124 1.248 1464 156 40 54 417 431 .169
18 370 363 96 279 108 178 171 101 64 164 .578 0 -.593 1.111 18 35 .889 1.508 1.125 .663 .622 1420 156 62 76 30 44 -.593
19 379 360 897 1815 1632 194 183 108 962 1070 .834 0 .101 1.756 58 75 .55 .933 1.819 1.072 1.519 1398 156 62 76 54 68 .101
20 395 365 85 261 70 247 191 113 41 154 .719 0 -1.043 .986 15 26 1.214 2.061 .824 .485 .517 1402 156 63 77 78 92 -1.043

Total number of rows: 4608

Table truncated, full table size 552 Kbytes.




Supplementary data files not provided
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