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Sample GSM472 Query DataSets for GSM472
Status Public on Jul 25, 2001
Title G27 genomic DNA vs astra/tigr ref
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 G27 Genomic DNA (wizard prep)
Organism Helicobacter pylori
Extracted molecule genomic DNA
 
 
Description Category: Genomic DNA
Subcategory: Strain Comparison
Scanning Software: ScanAlyze
Software version: 2.33
Scanning parameters:
Lot batch = hp2029
 
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 73 73 4 78 10 67 68 48 7 55 -.181 0 .82 1.5 2 8 .4 .566 2.5 1.766 -.245 1520 112 38 50 30 42 .82
2 82 70 56 5 73 51 36 4 40 .361 0 2 0 11 .509 1492 112 37 49 54 66
3 95 81 237 360 301 87 59 42 213 254 .561 0 -.157 1.107 88 72 .787 1.115 1.27 .897 .811 1527 80 38 48 76 86 -.157
4 72 71 64 184 128 60 56 40 90 130 .469 0 .498 1.39 25 31 .5 .708 2 1.412 1.105 1521 112 37 49 102 114 .498
5 66 64 78 175 128 51 47 33 90 124 .395 0 .213 .842 34 40 .609 .863 1.641 1.159 .767 1511 112 37 49 126 138 .213
6 71 66 699 342 291 57 51 36 206 242 .587 0 -1.766 .384 90 86 2.402 3.401 .416 .294 .235 1511 112 37 49 150 162 -1.766
7 70 68 48 115 60 59 55 39 42 81 .601 0 -.18 .922 35 35 .8 1.133 1.25 .883 .901 1521 112 36 48 174 186 -.18
8 67 66 47 136 86 55 50 35 61 96 .419 0 .37 .778 34 33 .547 .774 1.83 1.292 1.249 1521 112 36 48 198 210 .37
9 67 65 268 498 453 48 45 32 320 352 .583 0 .256 1.376 84 89 .592 .838 1.69 1.194 .993 1514 112 36 48 223 235 .256
10 73 72 76 143 96 48 47 33 68 101 .343 0 -.165 .8 45 46 .792 1.121 1.263 .892 .575 1493 112 36 48 247 259 -.165
11 84 74 66 138 88 51 50 35 62 97 .578 0 -.087 1.113 54 70 .75 1.062 1.333 .942 .941 1504 112 36 48 271 283 -.087
12 84 72 451 91 39 54 52 37 28 64 .446 0 -4.033 .091 88 53 11.564 16.374 .086 .061 .053 1511 112 36 48 295 307 -4.033
13 73 71 186 325 270 57 55 39 191 230 .471 0 .036 1.363 81 82 .689 .975 1.452 1.025 .692 1522 112 35 47 319 331 .036
14 73 72 295 553 492 63 61 43 347 391 .797 0 .236 1.755 69 84 .6 .849 1.668 1.178 1.259 1511 112 35 47 343 355 .236
15 75 74 115 259 194 66 65 46 137 183 .695 0 .253 1.763 67 83 .593 .839 1.687 1.191 .989 1519 112 35 47 367 379 .253
16 77 76 146 308 242 67 66 47 171 218 .795 0 .227 1.846 54 62 .603 .854 1.658 1.171 1.243 1517 112 35 47 392 404 .227
17 76 76 200 328 264 66 64 45 186 232 .8 0 -.101 1.345 59 62 .758 1.073 1.32 .932 1.088 1534 112 35 47 416 428 -.101
18 72 70 85 196 132 66 64 45 93 138 .781 0 .133 1.76 59 74 .644 .912 1.553 1.097 .976 1510 112 62 74 30 42 .133
19 71 70 306 465 407 64 58 41 287 328 .706 0 -.09 1.269 74 74 .752 1.065 1.33 .939 .996 1505 112 61 73 54 66 -.09
20 82 80 46 99 17 83 82 58 12 70 .455 0 -1.938 .664 29 14 2.706 3.831 .37 .261 .506 1507 112 61 73 78 90 -1.938

Total number of rows: 4608

Table truncated, full table size 521 Kbytes.




Supplementary data files not provided
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