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Sample GSM495 Query DataSets for GSM495
Status Public on Jul 25, 2001
Title CCUG 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 CCUG 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 = hp3009
 
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 90 88 1153 2608 2549 66 59 30 1307 1337 .727 0 .18 2.08 80 81 .452 .882 2.211 1.133 1.651 1522 112 49 61 49 61 .18
2 96 92 508 641 577 71 64 33 296 329 .69 0 -.78 1.172 66 66 .88 1.718 1.136 .582 .801 1509 112 49 61 73 85 -.78
3 96 92 623 1095 1030 70 65 33 528 561 .723 0 -.239 1.39 82 91 .605 1.18 1.653 .847 1.18 1509 112 49 61 97 109 -.239
4 96 91 292 570 505 72 65 33 259 292 .602 0 -.174 1.811 68 75 .578 1.128 1.729 .887 1.039 1509 112 49 61 121 133 -.174
5 94 91 41 127 65 66 62 32 33 65 .449 0 -.299 1.464 22 28 .631 1.231 1.585 .813 .707 1509 112 49 61 145 157 -.299
6 95 92 502 495 433 66 62 32 222 254 .773 0 -1.177 .783 66 66 1.159 2.262 .863 .442 .673 1509 112 49 61 169 181 -1.177
7 103 94 89 186 121 74 65 33 62 95 .592 0 -.521 1.087 26 35 .736 1.435 1.36 .697 .804 1509 112 49 61 193 205 -.521
8 102 94 30 109 43 75 66 34 22 56 .569 0 -.445 1.474 18 26 .698 1.361 1.433 .735 .728 1509 112 49 61 217 229 -.445
9 99 96 260 596 526 74 70 36 270 306 .56 0 .052 2.028 61 70 .494 .964 2.023 1.037 1.152 1499 112 49 61 241 253 .052
10 111 103 41 164 85 88 79 40 44 84 .472 0 .088 1.357 21 42 .482 .941 2.073 1.063 .747 1427 112 50 62 265 277 .088
11 121 111 31 169 77 101 92 47 39 87 .581 0 .348 1.385 11 20 .403 .785 2.484 1.273 1.264 1381 112 50 62 289 301 .348
12 133 123 941 234 134 109 100 51 69 120 .696 0 -3.776 .13 91 61 7.022 13.7 .142 .073 .135 1415 177 46 61 312 327 -3.776
13 144 136 306 206 97 117 109 56 50 106 .539 0 -2.622 .532 60 43 3.155 6.154 .317 .162 .183 1408 112 50 62 337 349 -2.622
14 145 140 153 466 346 129 120 62 177 239 .632 0 .213 1.938 40 53 .442 .863 2.261 1.159 1.393 1503 112 50 62 361 373 .213
15 161 153 108 299 152 156 147 75 78 153 .66 0 -.471 1.557 45 69 .711 1.386 1.407 .721 .826 1515 112 50 62 386 398 -.471
16 166 155 36 239 82 176 157 80 42 123 .47 0 .224 1.659 16 31 .439 .856 2.278 1.168 1.046 1491 112 50 62 410 422 .224
17 170 155 35 264 101 183 163 84 52 135 .539 0 .565 1.988 16 28 .347 .676 2.886 1.479 1.325 1513 112 50 62 434 446 .565
18 112 93 107 194 126 103 68 35 65 99 .568 0 -.728 .95 65 74 .849 1.657 1.178 .604 .712 1490 112 73 85 49 61 -.728
19 104 96 118 268 193 85 75 38 99 137 .676 0 -.254 1.401 35 51 .611 1.193 1.636 .838 1.066 1475 112 73 85 73 85 -.254
20 110 99 11 83 4 95 79 40 2 43 .583 0 -2.424 1.18 11 14 2.75 5.365 .364 .186 .803 1488 112 73 85 97 109 -2.424

Total number of rows: 4608

Table truncated, full table size 554 Kbytes.




Supplementary data files not provided
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