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Sample GSM480 Query DataSets for GSM480
Status Public on Jul 25, 2001
Title 292 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 2 ug 292genomic 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 = hp3035
 
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
1 126 110 1775 1802 1682 134 120 160 2243 2403 .808 0 .338 1.08 75 74 1.055 .791 .948 1.264 .774 1515 112 47 59 54 66 .338
2 114 109 287 443 323 121 120 160 431 591 .728 0 .587 1.087 58 60 .889 .666 1.125 1.502 .788 1505 112 47 59 78 90 .587
3 116 109 575 598 474 124 124 165 632 797 .769 0 .136 .889 64 57 1.213 .91 .824 1.099 .637 1508 112 47 59 102 114 .136
4 118 111 37 145 16 130 129 172 21 193 .364 0 -.817 .643 26 8 2.313 1.762 .432 .568 .228 1508 112 47 59 126 138 -.817
5 118 113 52 149 13 137 136 181 18 199 .449 0 -1.531 .463 33 7 4 2.889 .25 .346 .227 1508 112 47 59 150 162 -1.531
6 116 109 768 388 247 142 141 188 329 517 .604 0 -1.223 .33 86 78 3.109 2.334 .322 .428 .181 1526 112 47 59 174 186 -1.223
7 113 107 50 162 20 142 142 189 27 216 .511 0 -.889 .6 26 12 2.5 1.852 .4 .54 .235 1521 112 47 59 200 212 -.889
8 111 106 25 151 7 145 144 192 9 201 .37 0 -1.474 .632 19 4 3.571 2.778 .28 .36 .24 1509 112 47 59 224 236 -1.474
9 106 101 208 321 171 150 150 200 228 428 .762 0 .132 .861 53 45 1.216 .912 .822 1.096 .633 1509 112 47 59 248 260 .132
10 106 102 21 168 11 157 157 209 15 224 .383 0 -.485 .548 20 1 1.909 1.4 .524 .714 .216 1509 112 47 59 272 284 -.485
11 109 105 28 182 19 165 163 217 26 243 .603 0 -.107 1.05 19 6 1.474 1.077 .679 .929 .45 1498 112 48 60 296 308 -.107
12 120 109 243 179 8 177 171 228 11 239 .297 0 -4.465 .07 55 0 30.375 22.091 .033 .045 .028 1500 112 48 60 320 332 -4.465
13 125 113 116 205 26 182 179 239 34 273 .438 0 -1.771 .221 44 9 4.462 3.412 .224 .293 .154 1469 112 48 60 344 356 -1.771
14 125 115 239 351 174 176 177 236 232 468 .729 0 -.043 .673 42 33 1.374 1.03 .728 .971 .554 1499 112 48 60 368 380 -.043
15 121 116 56 198 21 176 177 236 28 264 .391 0 -1 .647 27 8 2.667 2 .375 .5 .155 1509 112 48 60 392 404 -1
16 121 115 54 215 35 181 180 240 47 287 .545 0 -.2 1.122 33 13 1.543 1.149 .648 .87 .396 1509 112 48 60 416 428 -.2
17 120 113 112 236 54 182 182 243 72 315 .429 0 -.637 .523 33 23 2.074 1.556 .482 .643 .182 1534 112 48 60 440 452 -.637
18 121 112 29 144 15 135 129 172 20 192 .445 0 -.536 .696 18 8 1.933 1.45 .517 .69 .308 1438 112 70 82 56 68 -.536
19 114 109 118 226 96 191 130 173 128 301 .752 0 .117 .779 37 33 1.229 .922 .814 1.085 .566 1418 112 71 83 80 92 .117
20 115 108 12 135 3 190 132 176 4 180 .296 0 -1.585 .818 8 2 4 3 .25 .333 .203 1477 112 71 83 104 116 -1.585

Total number of rows: 4608

Table truncated, full table size 545 Kbytes.




Supplementary data files not provided
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