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Sample GSM69880 Query DataSets for GSM69880
Status Public on Aug 16, 2005
Title G1 vs TIGR/Astra Genomic DNA
Sample type genomic
 
Channel 1
Source name TIGR/Astra Genomic DNA
Organism Helicobacter pylori
Characteristics TIGR/Astra Genomic DNA
Extracted molecule genomic DNA
Label Cy3
 
Channel 2
Source name G1 Genomic DNA
Organism Helicobacter pylori
Characteristics G1 Genomic DNA
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2902.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 Aug 15, 2005
Last update date Jan 05, 2007
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)
GSE3135 H. pylori strain comparisons

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 values 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 value of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized value 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 value of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized value 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
1 175 234 13 0 162 234 null null 14 1 null null null null null null null null 99 97 null null null null .692 1.444 null null 1.44 null 156 1107 1.457 .963 null null null 30 45 45 60 0 308 0 308 1.903 null null .525 null .929 null .929
2 52 24 14 0 38 24 null null 14 0 null null null null null null null null 86 76 null null null null 1.583 .632 null null .5 null 52 340 .664 .824 null null null 33 41 73 81 0 32 0 32 .832 null null 1.202 null -.265 null -.265
3 76 66 13 0 63 66 null null 13 0 null null null null null null null null 98 98 null null null null .955 1.048 null null .947 null 52 420 .882 .834 null null null 31 40 97 106 0 87 0 87 1.381 null null .724 null .465 null .465
4 19 2 12 0 7 2 null null 13 0 null null null null null null null null 45 16 null null null null 3.5 .286 null null .273 null 80 552 .189 .496 null null null 29 39 123 133 0 3 0 3 .377 null null 2.656 null -1.409 null -1.409
5 37 5 13 0 24 5 null null 13 0 null null null null null null null null 10 50 null null null null 4.8 .208 null null .25 null 32 176 .217 .662 null null null 32 38 148 154 0 7 0 7 .275 null null 3.642 null -1.865 null -1.865
6 119 38 16 0 103 38 null null 16 0 null null null null null null null null 10 92 null null null null 2.711 .369 null null .415 null 52 420 .357 .876 null null null 31 40 171 180 0 50 0 50 .486 null null 2.057 null -1.04 null -1.04
7 18 1 14 0 4 1 null null 14 0 null null null null null null null null 27 15 null null null null 4 .25 null null .5 null 80 552 .176 .363 null null null 29 39 195 205 0 1 0 1 .329 null null 3.035 null -1.602 null -1.602
8 13 0 13 0 null null null null 13 0 null null null null null null null null 13 80 null null null null null null null null .167 null 80 552 .013 .134 null null null 29 39 219 229 0 0 0 0 null null null null null null null null
9 35 21 14 0 21 21 null null 14 0 null null null null null null null null 67 67 null null null null 1 1 null null .857 null 52 332 .838 .748 null null null 30 38 245 253 0 28 0 28 1.318 null null .759 null .398 null .398
10 20 5 15 0 5 5 null null 15 0 null null null null null null null null 28 26 null null null null 1 1 null null .912 null 80 552 .445 .519 null null null 29 39 267 277 0 7 0 7 1.318 null null .759 null .398 null .398
11 18 1 16 0 2 1 null null 16 0 null null null null null null null null 22 10 null null null null 2 .5 null null .429 null 80 552 .023 .114 null null null 29 39 291 301 0 1 0 1 .659 null null 1.518 null -.602 null -.602
12 46 84 19 0 27 84 null null 19 0 null null null null null null null null 84 93 null null null null .321 3.111 null null 2.774 null 32 236 2.298 .777 null null null 31 38 316 323 0 111 0 111 4.1 null null .244 null 2.036 null 2.036
13 38 7 17 0 21 7 null null 17 0 null null null null null null null null 10 50 null null null null 3 .333 null null .467 null 12 104 .41 .753 null null null 31 36 342 347 0 9 0 9 .439 null null 2.277 null -1.187 null -1.187
14 73 43 16 0 57 43 null null 16 0 null null null null null null null null 93 93 null null null null 1.326 .754 null null .767 null 32 236 .645 .873 null null null 31 38 364 371 0 57 0 57 .994 null null 1.006 null -.009 null -.009
15 40 2 14 0 26 2 null null 14 0 null null null null null null null null 95 25 null null null null 13 .077 null null .133 null 80 552 .049 .265 null null null 29 39 388 398 0 3 0 3 .101 null null 9.865 null -3.302 null -3.302
16 19 3 14 0 5 3 null null 14 0 null null null null null null null null 33 28 null null null null 1.667 .6 null null .667 null 80 538 .288 .62 null null null 28 38 412 422 0 4 0 4 .791 null null 1.265 null -.339 null -.339
17 48 18 14 0 34 18 null null 15 0 null null null null null null null null 90 81 null null null null 1.889 .529 null null .712 null 32 176 .416 .72 null null null 32 38 438 444 0 24 0 24 .698 null null 1.433 null -.519 null -.519
18 24 1 13 0 11 1 null null 13 0 null null null null null null null null 52 13 null null null null 11 .091 null null .295 null 80 530 .048 .401 null null null 54 64 51 61 0 1 0 1 .12 null null 8.347 null -3.061 null -3.061
19 74 49 14 0 60 49 null null 15 0 null null null null null null null null 93 96 null null null null 1.224 .817 null null .766 null 32 176 .777 .866 null null null 57 63 78 84 0 65 0 65 1.076 null null .929 null .106 null .106
20 14 0 11 0 3 null null null 12 0 null null null null null null null null 37 60 null null null null null null null null .167 null 80 560 .009 .13 null null null 54 64 99 109 0 0 0 0 null null null null null null null null

Total number of rows: 4608

Table truncated, full table size 1063 Kbytes.




Supplementary data files not provided
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