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Sample GSM496 Query DataSets for GSM496
Status Public on Jul 25, 2001
Title G50 genomic DNA vs. Tigr/Astra reference III
Sample type genomic
 
Channel 1
Source name 1 ug Tigr genomic DNA, 1 ug Astra genomic DNA
Organism Helicobacter pylori
Extracted molecule genomic DNA
 
Channel 2
Source name 2 ug G50 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 = hp3010
 
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
1 172 122 1620 1201 1119 98 82 111 1512 1623 .726 0 -.1 .636 84 89 1.448 1.071 .691 .933 .501 1522 112 61 73 38 50 -.1
2 125 124 726 342 261 82 81 109 353 462 .752 0 -1.04 .369 64 52 2.782 2.057 .36 .486 .272 1507 112 61 73 62 74 -1.04
3 122 121 755 525 446 80 79 107 602 709 .764 0 -.327 .64 73 74 1.693 1.254 .591 .797 .45 1509 112 61 73 86 98 -.327
4 118 114 478 332 257 77 75 101 348 449 .675 0 -.458 .553 72 69 1.86 1.374 .538 .728 .35 1509 112 61 73 110 122 -.458
5 115 112 68 119 44 77 75 101 60 161 .72 0 -.181 .605 29 25 1.545 1.133 .647 .882 .452 1509 112 61 73 134 146 -.181
6 121 115 605 242 166 78 76 103 224 327 .686 0 -1.433 .295 68 58 3.645 2.701 .274 .37 .171 1509 112 61 73 158 170 -1.433
7 117 112 146 141 69 74 72 97 94 191 .54 0 -.635 .515 39 27 2.116 1.553 .473 .644 .301 1509 112 61 73 182 194 -.635
8 109 106 61 88 18 72 70 95 24 119 .662 0 -1.346 .341 26 16 3.389 2.542 .295 .393 .202 1509 112 61 73 206 218 -1.346
9 109 106 348 343 275 70 68 92 372 464 .622 0 .096 .732 64 63 1.265 .935 .79 1.069 .514 1499 112 61 73 230 242 .096
10 110 108 61 116 49 69 67 91 66 157 .641 0 .114 .758 25 29 1.245 .924 .803 1.082 .525 1448 112 61 73 254 266 .114
11 122 115 60 107 37 75 70 95 50 145 .466 0 -.263 .909 21 24 1.622 1.2 .617 .833 .283 1406 112 61 73 278 290 -.263
12 138 124 1214 234 163 75 71 96 220 316 .185 0 -2.464 .11 88 68 7.448 5.518 .134 .181 .087 1405 177 58 73 301 316 -2.464
13 142 129 239 210 140 73 70 95 189 284 .538 0 -.339 .551 65 55 1.707 1.265 .586 .791 .325 1409 112 61 73 325 337 -.339
14 127 122 277 220 150 71 70 95 202 297 .61 0 -.456 .463 48 41 1.847 1.371 .542 .729 .32 1492 112 61 73 349 361 -.456
15 123 118 81 109 39 73 70 95 52 147 .359 0 -.639 .647 31 25 2.077 1.558 .481 .642 .147 1506 112 61 73 373 385 -.639
16 130 122 39 97 26 79 71 96 35 131 .388 0 -.156 .544 17 21 1.5 1.114 .667 .897 .223 1490 112 61 73 397 409 -.156
17 140 126 51 106 35 82 71 96 47 143 .574 0 -.118 .539 23 29 1.457 1.085 .686 .922 .402 1513 112 61 73 421 433 -.118
18 120 115 68 168 88 83 80 108 119 227 .365 0 .807 1 43 60 .773 .571 1.294 1.75 .308 1476 112 85 97 39 51 .807
19 128 121 60 139 56 85 83 112 76 188 .479 0 .341 .6 20 25 1.071 .789 .933 1.267 .291 1462 112 85 97 62 74 .341
20 134 129 84 88 85 115 114 .041 0 1.114 0 2 .024 1488 112 85 97 86 98

Total number of rows: 4608

Table truncated, full table size 542 Kbytes.




Supplementary data files not provided

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