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Sample GSM498 Query DataSets for GSM498
Status Public on Jul 25, 2001
Title 326 genomic DNA vs. Tigr/Astra reference III
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 326 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 = hp3012
 
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 77 73 919 1236 1199 47 37 24 791 815 .68 0 -.217 1.287 80 83 .766 1.162 1.305 .861 .966 1522 112 61 73 39 51 -.217
2 78 77 456 296 255 43 41 27 168 195 .6 0 -1.439 .588 62 61 1.788 2.711 .559 .369 .322 1509 112 61 73 63 75 -1.439
3 76 75 340 502 463 40 39 26 305 331 .741 0 -.155 1.281 66 78 .734 1.113 1.362 .898 .989 1509 112 61 73 87 99 -.155
4 75 75 123 196 157 40 39 26 104 129 .664 0 -.248 1 45 55 .783 1.188 1.276 .842 .904 1509 112 61 73 111 123 -.248
5 77 76 21 61 22 40 39 26 15 40 .376 0 -.533 .974 15 24 .955 1.447 1.048 .691 .318 1507 112 61 73 135 147 -.533
6 80 77 381 213 173 42 40 26 114 140 .687 0 -1.739 .447 65 66 2.202 3.339 .454 .3 .293 1497 112 61 73 159 171 -1.739
7 78 77 95 107 66 42 41 27 44 71 .451 0 -1.126 .706 35 39 1.439 2.182 .695 .458 .291 1499 112 61 73 182 194 -1.126
8 78 77 32 67 26 42 41 27 17 44 .453 0 -.9 .9 19 28 1.231 1.866 .813 .536 .333 1509 112 61 73 206 218 -.9
9 84 81 168 279 235 46 44 29 155 184 .451 0 -.116 1.291 53 67 .715 1.084 1.399 .923 .569 1508 112 61 73 230 242 -.116
10 92 87 26 73 25 51 48 32 16 48 .433 0 -.657 .8 17 21 1.04 1.577 .962 .634 .489 1427 112 61 73 254 266 -.657
11 103 97 34 86 31 59 55 36 20 57 .519 0 -.734 1 16 21 1.097 1.663 .912 .601 .449 1379 112 61 73 278 290 -.734
12 111 104 423 591 528 70 63 42 348 390 .7 0 -.28 1.333 93 97 .801 1.215 1.248 .823 .78 1415 177 58 73 301 316 -.28
13 118 111 98 183 115 74 68 45 76 121 .399 0 -.37 .897 37 45 .852 1.292 1.173 .774 .412 1427 112 61 73 326 338 -.37
14 117 114 131 222 154 72 68 45 102 146 .677 0 -.367 1.4 33 39 .851 1.29 1.176 .775 .8 1497 112 61 73 350 362 -.367
15 116 112 22 98 30 72 68 45 20 65 .446 0 -.153 1.043 18 23 .733 1.112 1.364 .899 .54 1506 112 61 73 374 386 -.153
16 121 110 13 87 18 83 69 46 12 57 .369 0 -.131 .811 9 21 .722 1.095 1.385 .913 .478 1490 112 61 73 398 410 -.131
17 127 107 34 109 39 92 70 46 26 72 .354 0 -.402 1.113 23 33 .872 1.322 1.147 .757 .416 1513 112 61 73 422 434 -.402
18 82 75 81 124 84 49 40 26 55 82 .698 0 -.548 1.031 58 66 .964 1.462 1.037 .684 .675 1490 112 85 97 39 51 -.548
19 82 79 60 131 86 48 45 30 57 86 .657 0 -.081 1.111 29 40 .698 1.058 1.433 .945 .893 1475 112 85 97 63 75 -.081
20 81 78 9 53 9 47 44 29 6 35 .46 0 -.6 .82 8 16 1 1.516 1 .66 .308 1488 112 85 97 87 99 -.6

Total number of rows: 4608

Table truncated, full table size 542 Kbytes.




Supplementary data files not provided

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