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Sample GSM482 Query DataSets for GSM482
Status Public on Jul 25, 2001
Title Sydney wizard prep genomic DNA vs TIGR/Astra reference
Sample type genomic
 
Channel 1
Source name 1 ug tigr genomic DNA, 1ug Asgra genomic DNA
Organism Helicobacter pylori
Extracted molecule genomic DNA
 
Channel 2
Source name 2 ug sydney strain 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 = hp3098
 
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
1 167 138 2299 2836 2745 110 91 91 2745 2836 .907 0 .256 1.24 99 99 .838 .838 1.194 1.194 1.128 1246 316 52 72 70 90 .256
2 198 175 956 702 588 129 114 114 588 702 .884 0 -.701 .536 100 94 1.626 1.626 .615 .615 .646 1441 112 51 63 98 110 -.701
3 193 184 625 717 600 122 117 117 600 717 .814 0 -.059 .997 79 73 1.042 1.042 .96 .96 .833 1443 112 54 66 122 134 -.059
4 190 177 107 198 87 117 111 111 87 198 .783 0 -.299 .783 46 52 1.23 1.23 .813 .813 .631 1485 112 52 64 144 156 -.299
5 197 185 114 185 78 114 107 107 78 185 .772 0 -.547 .671 45 52 1.462 1.462 .684 .684 .507 1516 112 52 64 168 180 -.547
6 230 208 921 477 370 115 107 107 370 477 .738 0 -1.316 .403 85 90 2.489 2.489 .402 .402 .282 1456 177 51 66 193 208 -1.316
7 215 201 80 154 52 106 102 102 52 154 .771 0 -.621 .644 32 40 1.538 1.538 .65 .65 .455 1483 112 52 64 218 230 -.621
8 178 178 16 109 14 96 95 95 14 109 .625 0 -.193 .625 8 15 1.143 1.143 .875 .875 .358 1509 112 52 64 242 254 -.193
9 168 167 198 320 228 94 92 92 228 320 .78 0 .204 1.226 52 69 .868 .868 1.152 1.152 .785 1509 112 52 64 266 278 .204
10 163 160 75 180 89 94 91 91 89 180 .744 0 .247 1.195 33 52 .843 .843 1.187 1.187 .767 1509 112 52 64 290 302 .247
11 166 156 26 131 39 97 92 92 39 131 .731 0 .585 .871 16 33 .667 .667 1.5 1.5 .59 1509 112 52 64 314 326 .585
12 170 157 389 149 52 116 97 97 52 149 .543 0 -2.903 .12 62 38 7.481 7.481 .134 .134 .141 1509 112 52 64 338 350 -2.903
13 181 161 76 177 74 126 103 103 74 177 .82 0 -.038 1 36 46 1.027 1.027 .974 .974 .701 1484 112 52 64 362 374 -.038
14 194 173 443 716 598 132 118 118 598 716 .629 0 .433 1.392 98 100 .741 .741 1.35 1.35 .743 1453 112 55 67 384 396 .433
15 203 176 50 175 52 139 123 123 52 175 .592 0 .057 1.187 24 33 .962 .962 1.04 1.04 .538 1521 112 52 64 410 422 .057
16 173 167 36 159 44 120 115 115 44 159 .652 0 .29 .923 23 25 .818 .818 1.222 1.222 .63 1511 112 52 64 434 446 .29
17 171 167 70 181 65 121 116 116 65 181 .74 0 -.107 .811 29 27 1.077 1.077 .929 .929 .611 1533 112 53 65 458 470 -.107
18 136 115 28 96 34 84 62 62 34 96 .504 0 .28 1.301 17 26 .824 .824 1.214 1.214 .514 1343 112 75 87 74 86 .28
19 159 125 216 232 160 99 72 72 160 232 .895 0 -.433 .809 40 42 1.35 1.35 .741 .741 .67 1443 112 75 87 98 110 -.433
20 158 133 77 94 79 79 77 .595 0 .96 10 11 .388 1459 112 75 87 122 134

Total number of rows: 4608

Table truncated, full table size 542 Kbytes.




Supplementary data files not provided
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