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Sample GSM78735 Query DataSets for GSM78735
Status Public on Oct 20, 2005
Title AR28 vs Tigr/Astra reference
Sample type genomic
 
Channel 1
Source name 1ug Tigr genomic DNA + 1 ug Astra DNA
Organism Helicobacter pylori
Characteristics 1ug Tigr genomic DNA + 1 ug Astra DNA
Extracted molecule genomic DNA
Label Cy3
 
Channel 2
Source name 2 ug AR28 genomic DNA
Organism Helicobacter pylori
Characteristics 2 ug AR28 genomic DNA
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-05/6448.gif
Data processing VALUE is Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Oct 19, 2005
Last update date Feb 20, 2008
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)
GSE3479 Helicobacter pylori bacterial populations

Data table header descriptions
ID_REF ID_REF
CH1I_MEAN Mean feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEAN Mean feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEDIAN The median feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_MEDIAN The median feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH1D_MEAN The mean feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2D_MEAN .The mean feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1I_MEDIAN Median feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEDIAN Median feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEAN The mean feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Background
CH2B_MEAN The mean feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Background
CH1D_MEDIAN The median feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH2D_MEDIAN The median feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH1_PER_SAT The percentage of feature pixels at wavelength 532 nm that are saturated.; Type: integer; Scale: linear_scale
CH2_PER_SAT The percentage of feature pixels at wavelength 635 nm that are saturated.; Type: integer; Scale: linear_scale
CH1I_SD The standard deviation of the feature intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2I_SD The standard deviation of the feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1B_SD The standard deviation of the feature background intensity at wavelength 532 nm.; Type: float; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_SD The standard deviation of the feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
PERGTBCH1I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 635 nm.; Type: integer; Scale: linear_scale
PERGTBCH1I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
SUM_MEAN The sum of the arithmetic mean intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
SUM_MEDIAN The sum of the median intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
RAT1_MEAN Ratio of the arithmetic mean intensities of each spot for each wavelength, with the median background subtracted. Channel 1/Channel 2 ratio, (CH1I_MEAN - CH1B_MEDIAN)/(CH2I_MEAN - CH2B_MEDIAN) or Green/Red ratio.; Type: float; Scale: linear_scale
RAT2_MEAN The ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_MEDIAN The ratio of the median intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEAN The geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEDIAN The median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_SD The geometric standard deviation of the pixel intensity ratios.; Type: float; Scale: linear_scale
TOT_SPIX The total number of feature pixels.; Type: integer; Scale: linear_scale
TOT_BPIX The total number of background pixels.; Type: integer; Scale: linear_scale
REGR The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature.; Type: float; Scale: linear_scale
CORR The correlation between channel1 (Cy3) & Channel 2 (Cy5) pixels within the spot, and is a useful quality control parameter. Generally, high LOG_RAT2N_MEDIANs imply better fit & good spot quality.; Type: float; Scale: linear_scale
DIAMETER The diameter in um of the feature-indicator.; Type: integer; Scale: linear_scale
X_COORD X-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
Y_COORD Y-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
TOP Box top: int(((centerX - radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
BOT Box bottom: int(((centerX + radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
LEFT Box left: int(((centerY - radius) - yoffset) / pixelSize).; Type: integer; Scale: linear_scale
RIGHT Box right: int(((centerY + radius) - yoffset) / pixelSize); Type: integer; Scale: linear_scale
FLAG The type of flag associated with a feature: -100 = user-flagged null spot; -50 = software-flagged null spot; 0 = spot valid.; Type: integer; Scale: linear_scale
CH2IN_MEAN Normalized LOG_RAT2N_MEDIAN of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized LOG_RAT2N_MEDIAN of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized LOG_RAT2N_MEDIAN of mean Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
RAT2N_MEAN Type: float; Scale: linear_scale
CH2IN_MEDIAN Normalized LOG_RAT2N_MEDIAN of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized LOG_RAT2N_MEDIAN of median Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEDIAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale
RAT1N_MEAN Ratio of the means of Channel 1 (usually 532 nm) intensity to normalized Channel 2 (usually 635 nm) intensity with median background subtracted (CH1D_MEAN/CH2DN_MEAN). Channel 1/Channel 2 ratio normalized or Green/Red ratio normalized.; Type: float; Scale: linear_scale
RAT2N_MEDIAN Channel 2/Channel 1 ratio normalized, RAT2_MEDIAN/Normalization factor or Red/Green median ratio normalized.; Type: float; Scale: linear_scale
VALUE same as UNF_VALUE but with flagged values removed
LOG_RAT2N_MEDIAN Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEDIAN)].; Type: float; Scale: log_base_2
UNF_VALUE Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEAN)].; Type: float; Scale: log_base_2

Data table
ID_REF CH1I_MEAN CH2I_MEAN CH1B_MEDIAN CH2B_MEDIAN CH1D_MEAN CH2D_MEAN CH1I_MEDIAN CH2I_MEDIAN CH1B_MEAN CH2B_MEAN CH1D_MEDIAN CH2D_MEDIAN CH1_PER_SAT CH2_PER_SAT CH1I_SD CH2I_SD CH1B_SD CH2B_SD PERGTBCH1I_1SD PERGTBCH2I_1SD PERGTBCH1I_2SD PERGTBCH2I_2SD SUM_MEAN SUM_MEDIAN RAT1_MEAN RAT2_MEAN RAT2_MEDIAN PIX_RAT2_MEAN PIX_RAT2_MEDIAN RAT2_SD TOT_SPIX TOT_BPIX REGR CORR DIAMETER X_COORD Y_COORD TOP BOT LEFT RIGHT FLAG CH2IN_MEAN CH2BN_MEDIAN CH2DN_MEAN RAT2N_MEAN CH2IN_MEDIAN CH2DN_MEDIAN RAT1N_MEAN RAT2N_MEDIAN VALUE LOG_RAT2N_MEDIAN UNF_VALUE
1 2515 1906 53 199 2462 1707 null null 54 202 null null null null null null null null 100 99 null null null null 1.442 .693 null null .69 null 256 1644 .683 .98 null null null 48 66 53 71 0 2094 218 1876 .762 null null 1.312 null -.392 null -.392
2 1218 739 59 201 1159 538 null null 68 213 null null null null null null null null 100 98 null null null null 2.154 .464 null null .44 null 52 420 .433 .9 null null null 52 61 82 91 0 812 220 592 .511 null null 1.958 null -.969 null -.969
3 856 812 51 203 805 609 null null 55 205 null null null null null null null null 98 97 null null null null 1.322 .757 null null .741 null 80 560 .745 .95 null null null 53 63 108 118 0 892 223 669 .831 null null 1.203 null -.267 null -.267
4 325 399 54 200 271 199 null null 61 205 null null null null null null null null 100 84 null null null null 1.362 .734 null null .76 null 32 236 .69 .76 null null null 53 60 131 138 0 438 219 219 .808 null null 1.237 null -.307 null -.307
5 187 356 58 210 129 146 null null 60 218 null null null null null null null null 100 81 null null null null .884 1.132 null null 1.115 null 32 236 1.007 .66 null null null 54 61 157 164 0 391 230 161 1.248 null null .801 null .32 null .32
6 1029 453 59 215 970 238 null null 75 223 null null null null null null null null 82 75 null null null null 4.076 .245 null null .292 null 120 932 .263 .83 null null null 50 63 179 192 0 497 236 261 .269 null null 3.716 null -1.894 null -1.894
7 435 499 80 216 355 283 null null 85 225 null null null null null null null null 91 91 null null null null 1.254 .797 null null .821 null 12 104 .76 .75 null null null 54 59 205 210 0 548 237 311 .876 null null 1.141 null -.191 null -.191
8 104 235 54 205 50 30 null null 58 211 null null null null null null null null 47 25 null null null null 1.667 .6 null null 1.433 null 80 552 .702 .41 null null null 50 60 227 237 0 258 225 33 .66 null null 1.515 null -.599 null -.599
9 678 801 60 219 618 582 null null 83 233 null null null null null null null null 96 96 null null null null 1.062 .942 null null .9 null 32 236 .826 .86 null null null 51 58 252 259 0 880 240 640 1.036 null null .966 null .05 null .05
10 218 391 58 210 160 181 null null 59 217 null null null null null null null null 98 84 null null null null .884 1.131 null null 1.141 null 52 340 1.056 .7 null null null 53 61 277 285 0 429 230 199 1.244 null null .804 null .315 null .315
11 244 472 75 250 169 222 null null 81 256 null null null null null null null null 91 83 null null null null .761 1.314 null null 1.476 null 12 104 1.072 .62 null null null 54 59 301 306 0 518 274 244 1.444 null null .693 null .53 null .53
12 1016 299 67 213 949 86 null null 99 218 null null null null null null null null 94 59 null null null null 11.035 .091 null null .123 null 52 420 .094 .55 null null null 51 60 324 333 0 328 234 94 .099 null null 10.096 null -3.336 null -3.336
13 333 341 61 211 272 130 null null 63 216 null null null null null null null null 100 78 null null null null 2.092 .478 null null .564 null 52 420 .484 .71 null null null 52 61 349 358 0 374 231 143 .526 null null 1.902 null -.928 null -.928
14 705 833 61 215 644 618 null null 88 239 null null null null null null null null 100 98 null null null null 1.042 .96 null null .989 null 52 420 .942 .9 null null null 51 60 372 381 0 915 236 679 1.054 null null .948 null .076 null .076
15 171 316 59 214 112 102 null null 65 221 null null null null null null null null 90 62 null null null null 1.098 .911 null null 1.396 null 32 230 .357 .26 null null null 50 57 396 403 0 347 235 112 1 null null 1 null 0 null 0
16 405 440 57 213 348 227 null null 58 216 null null null null null null null null 91 83 null null null null 1.533 .652 null null .675 null 12 104 .67 .84 null null null 55 60 422 427 0 483 234 249 .716 null null 1.398 null -.483 null -.483
17 177 345 54 197 123 148 null null 56 201 null null null null null null null null 81 71 null null null null .831 1.203 null null 1.298 null 32 176 .732 .57 null null null 54 60 446 452 0 379 216 163 1.325 null null .755 null .406 null .406
18 80 241 53 205 27 36 null null 53 210 null null null null null null null null 36 31 null null null null .75 1.333 null null 3 null 80 497 .695 .38 null null null 74 84 58 68 0 264 225 39 1.444 null null .692 null .531 null .531
19 778 714 55 212 723 502 null null 56 217 null null null null null null null null 100 96 null null null null 1.44 .694 null null .708 null 52 340 .664 .89 null null null 77 85 84 92 0 784 232 552 .763 null null 1.31 null -.389 null -.389
20 231 283 55 218 176 65 null null 55 218 null null null null null null null null 81 37 null null null null 2.708 .369 null null .5 null 32 236 .463 .63 null null null 76 83 109 116 0 310 239 71 .403 null null 2.479 null -1.31 null -1.31

Total number of rows: 4608

Table truncated, full table size 1111 Kbytes.




Supplementary data files not provided
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