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Sample GSM481 Query DataSets for GSM481
Status Public on Jul 25, 2001
Title G27 genomic DNA vs. TIGR/Astra reference
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 2ug G27 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 = hp3044
 
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
1 199 181 2141 4607 4500 159 107 59 2475 2534 .808 0 .209 2.055 90 94 .476 .865 2.102 1.156 .774 1412 225 54 71 67 84 .209
2 211 184 2172 2607 2498 124 109 60 1374 1434 .728 0 -.661 1.79 68 80 .869 1.581 1.15 .632 .788 1466 112 55 67 93 105 -.661
3 187 182 787 1564 1454 119 110 60 800 860 .722 0 .023 1.554 56 67 .541 .984 1.848 1.016 1.221 1505 112 55 67 117 129 .023
4 180 177 69 225 117 115 108 59 64 124 .685 0 -.101 1.771 20 35 .59 1.072 1.696 .933 1.106 1505 112 55 67 141 153 -.101
5 176 174 44 154 51 107 103 57 28 85 .695 0 -.65 1.069 16 27 .863 1.569 1.159 .637 .662 1527 112 54 66 165 177 -.65
6 190 176 1192 828 723 119 105 58 398 455 .681 0 -1.584 .592 82 84 1.649 2.998 .607 .334 .447 1521 112 54 66 191 203 -1.584
7 178 172 48 181 74 113 107 59 41 100 .694 0 -.238 1.566 21 34 .649 1.179 1.542 .848 .993 1508 112 54 66 215 227 -.238
8 171 170 11 133 28 108 105 58 15 73 .476 0 .485 1.583 9 21 .393 .714 2.545 1.4 .7 1511 112 53 65 239 251 .485
9 171 169 277 713 609 108 104 57 335 392 .641 0 .274 2.033 50 63 .455 .827 2.199 1.209 1.355 1509 112 53 65 263 275 .274
10 175 171 40 172 65 118 107 59 36 95 .68 0 -.162 1.679 20 33 .615 1.119 1.625 .894 1.163 1509 112 53 65 287 299 -.162
11 176 172 38 172 67 119 105 58 37 95 .506 0 -.044 1.642 19 33 .567 1.031 1.763 .97 .735 1508 112 53 65 311 323 -.044
12 183 176 510 240 126 130 114 63 69 132 .624 0 -2.88 .256 61 42 4.048 7.36 .247 .136 .198 1511 112 52 64 335 347 -2.88
13 191 179 133 364 243 138 121 67 134 200 .657 0 .007 1.73 39 53 .547 .995 1.827 1.005 1.109 1506 112 52 64 359 371 .007
14 186 175 365 901 783 131 118 65 431 495 .657 0 .238 1.735 38 48 .466 .848 2.145 1.18 1.363 1506 112 52 64 383 395 .238
15 185 177 90 190 76 127 114 63 42 104 .72 0 -1.107 .96 24 27 1.184 2.153 .844 .464 .579 1511 112 51 63 407 419 -1.107
16 185 175 102 350 237 123 113 62 130 192 .604 0 .354 1.379 25 40 .43 .783 2.324 1.278 1.388 1507 112 51 63 431 443 .354
17 181 169 208 468 355 123 113 62 195 257 .564 0 -.091 1.346 34 48 .586 1.065 1.707 .939 .817 1532 112 51 63 455 467 -.091
18 178 176 41 193 90 114 103 57 49 106 .333 0 .272 1.486 19 36 .456 .828 2.195 1.207 .715 1463 112 80 92 72 84 .272
19 179 176 205 482 375 115 107 59 206 265 .677 0 .009 1.565 39 49 .547 .994 1.829 1.006 1.166 1490 112 79 91 96 108 .009
20 176 175 21 153 46 111 107 59 25 84 .435 0 .269 1.5 7 24 .457 .83 2.19 1.205 .605 1491 112 79 91 120 132 .269

Total number of rows: 4608

Table truncated, full table size 566 Kbytes.




Supplementary data files not provided
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