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Sample GSM479 Query DataSets for GSM479
Status Public on Jul 25, 2001
Title Tigr wizard prep genomic DNA vs TIGR/Astra reference
Sample type genomic
 
Channel 1
Source name 1 ug TIGR genomic DNA, 1ug Astra genomic DNA
Organism Helicobacter pylori
Extracted molecule genomic DNA
 
Channel 2
Source name 2 ug TIGR genomic DNA, wizard prep
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 = hp3001
 
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
1 153 132 1036 1099 999 117 100 119 1189 1308 .689 0 .199 .868 64 77 1.037 .871 .964 1.148 .663 1525 112 76 88 45 57 .199
2 155 133 1322 1910 1806 120 104 124 2150 2274 .791 0 .702 1.128 82 83 .732 .615 1.366 1.626 1.13 1505 112 76 88 69 81 .702
3 152 130 1359 1461 1362 113 99 118 1621 1739 .75 0 .254 .935 86 88 .998 .838 1.002 1.193 .775 1505 112 76 88 93 105 .254
4 146 130 451 544 444 111 100 119 529 648 .668 0 .23 .981 75 73 1.016 .853 .984 1.173 .653 1505 112 76 88 117 129 .23
5 156 141 132 248 141 120 107 127 168 295 .638 0 .348 .991 45 60 .936 .786 1.068 1.273 .554 1505 112 76 88 141 153 .348
6 194 170 277 504 376 145 128 152 448 600 .67 0 .694 1.055 73 73 .737 .618 1.357 1.617 .97 1513 112 77 89 165 177 .694
7 225 199 235 402 262 158 140 167 312 479 .473 0 .409 1.018 64 64 .897 .753 1.115 1.328 .573 1520 112 77 89 191 203 .409
8 263 224 84 232 77 183 155 185 91 276 .318 0 .115 .733 35 41 1.091 .923 .917 1.083 .265 1509 112 77 89 215 227 .115
9 305 259 479 722 533 219 189 225 635 860 .69 0 .407 1.15 71 69 .899 .754 1.113 1.326 .787 1509 112 77 89 239 251 .407
10 332 284 228 406 196 245 210 250 233 483 .468 0 .031 .691 53 49 1.163 .979 .86 1.022 .449 1509 112 77 89 263 275 .031
11 357 310 178 403 168 277 235 280 200 480 .605 0 .168 1.024 47 49 1.06 .89 .944 1.124 .621 1509 112 77 89 287 299 .168
12 358 322 511 1406 1159 289 247 294 1380 1674 .777 0 1.433 2.401 65 75 .441 .37 2.268 2.701 1.66 1509 112 77 89 311 323 1.433
13 368 327 431 513 262 289 251 299 312 611 .488 0 -.466 .661 75 66 1.645 1.381 .608 .724 .297 1509 112 77 89 335 347 -.466
14 358 312 318 535 290 277 245 292 345 637 .634 0 .118 .901 66 64 1.097 .922 .912 1.085 .621 1509 112 77 89 359 371 .118
15 334 289 97 344 119 260 225 268 142 410 .621 0 .55 1.358 38 51 .815 .683 1.227 1.464 .603 1509 112 77 89 383 395 .55
16 344 272 154 357 148 289 209 249 176 425 .67 0 .193 .878 40 50 1.041 .875 .961 1.143 .655 1509 112 77 89 407 419 .193
17 370 262 233 424 232 312 192 229 276 505 .868 0 .244 .957 54 53 1.004 .844 .996 1.185 .867 1534 112 77 89 431 443 .244
18 193 162 102 243 114 144 129 154 135 289 .414 0 .404 .955 41 53 .895 .756 1.118 1.324 .38 1502 112 100 112 48 60 .404
19 222 181 123 256 119 163 137 163 142 305 .592 0 .207 .757 33 31 1.034 .866 .967 1.154 .476 1489 112 100 112 72 84 .207
20 229 184 44 206 67 166 139 165 80 245 .529 0 .862 .791 22 32 .657 .55 1.523 1.818 .636 1490 112 100 112 96 108 .862

Total number of rows: 4608

Table truncated, full table size 562 Kbytes.




Supplementary data files not provided
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