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Sample GSM474 Query DataSets for GSM474
Status Public on Jul 25, 2001
Title TIGR OD=0.5 Brucella Broth
Sample type genomic
 
Channel 1
Source name TIGR ASTRA 50 50 2 ug total
Organism Helicobacter pylori
Extracted molecule genomic DNA
 
Channel 2
Source name TIGR cDNA
Organism Helicobacter pylori
Extracted molecule genomic DNA
 
 
Description Category: Cell-cycle
Subcategory: Strain Comparison
Scanning Software: ScanAlyze
Software version: 2.33
Scanning parameters:
Lot batch = hp2002
 
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 (1)
GSE6 Genetic diversity among Helicobacter pylori strains

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 58 24 3688 2621 2394 255 227 258 2720 2978 .81 0 -.439 .666 100 96 1.541 1.356 .649 .738 .599 1474 156 190 204 65 79 -.439
2 39 24 563 396 188 220 208 236 214 450 .803 0 -1.396 .364 87 62 2.995 2.631 .334 .38 .406 1428 156 191 205 90 104 -1.396
3 30 22 1726 1293 1062 226 231 263 1206 1469 .875 0 -.517 .642 92 75 1.625 1.431 .615 .699 .563 1422 156 191 205 114 128 -.517
4 26 21 158 257 6 241 251 285 7 292 .801 0 -4.496 .404 92 14 26.333 22.571 .038 .044 .617 1420 156 192 206 138 152 -4.496
5 22 20 16 212 227 237 269 241 .469 0 1.854 42 8 1.74 1425 156 192 206 162 176
6 23 21 846 614 413 206 201 228 470 698 .897 0 -.848 .48 86 53 2.048 1.8 .488 .556 .495 1417 156 193 207 186 200 -.848
7 23 21 78 183 7 188 176 200 8 208 .724 0 -3.285 .494 76 10 11.143 9.75 .09 .103 .577 1423 156 193 207 210 224 -3.285
8 23 21 21 174 213 212 241 198 .056 0 2 59 0 .102 1447 156 193 207 234 248
9 29 23 678 566 332 230 234 266 377 643 .79 0 -.847 .501 94 61 2.042 1.798 .49 .556 .539 1428 156 194 208 259 273 -.847
10 34 27 24 184 225 230 261 209 .505 0 1.074 46 2 .772 1422 156 194 208 283 297
11 36 31 73 215 218 223 253 244 .649 0 .4 70 7 .579 1420 156 195 209 307 321
12 37 34 584 511 260 251 251 285 296 581 .692 0 -.98 .425 94 67 2.246 1.973 .445 .507 .453 1425 156 195 209 331 345 -.98
13 40 35 470 276 13 262 263 299 15 314 .502 0 -4.97 .132 85 14 36.154 31.333 .028 .032 .147 1417 156 196 210 355 369 -4.97
14 44 38 570 2603 2346 260 257 292 2666 2958 .834 0 2.226 3.9 88 88 .243 .214 4.116 4.677 3.416 1420 156 196 210 379 393 2.226
15 51 45 55 901 675 250 226 257 767 1024 .516 0 3.802 12.47 73 97 .081 .072 12.273 13.945 4.321 1423 156 196 210 403 417 3.802
16 55 52 26 192 226 203 231 218 .699 0 .797 39 5 1.023 1429 156 197 211 427 441
17 56 54 163 428 187 243 241 274 212 486 .794 0 .379 1.22 60 37 .872 .769 1.147 1.301 1.36 1474 156 197 211 452 466 .379
18 24 20 110 550 266 283 284 323 302 625 .762 0 1.457 1.852 98 50 .414 .364 2.418 2.745 2.788 1432 156 215 229 65 79 1.457
19 23 20 221 357 157 218 200 227 179 406 .808 0 -.304 .856 60 34 1.408 1.235 .71 .81 .742 1395 156 215 229 89 103 -.304
20 25 20 16 160 226 230 261 182 .413 0 .83 41 1 .626 1393 156 215 229 113 127

Total number of rows: 4608

Table truncated, full table size 540 Kbytes.




Supplementary data files not provided
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