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Sample GSM90254 Query DataSets for GSM90254
Status Public on Dec 31, 2005
Title 11168 orig vs. seq 1
Sample type genomic
 
Channel 1
Source name 0.5 ug sequenced 11168 DNA
Organism Campylobacter jejuni
Characteristics 0.5 ug sequenced 11168 DNA
Extracted molecule genomic DNA
Label Cy3
 
Channel 2
Source name 0.5 ug original 11168 DNA
Organism Campylobacter jejuni
Characteristics 0.5 ug original 11168 DNA
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28772.gif
Data processing VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Dec 30, 2005
Last update date Sep 05, 2013
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 GPL2791
Series (2)
GSE3954 Genomotyping of 11168-GS vs. 11168-O
GSE4387 Comparison of the genome-sequenced variant of Campylobacter jejuni NCTC 11168 and the original clonal clinical isolate

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
LOG_RAT2N_MEAN 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
VALUE 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

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 LOG_RAT2N_MEAN VALUE
1 225 120 151 96 74 24 153 85 155 102 2 -11 0 0 213 103 32 38 23 15 17 15 98 -9 3.083 .324 null .723 .512 3.641 80 518 .45 .83 100 2210 14130 36 46 40 50 -100 164 132 33 .444 116 null 2.251 null -1.17 null
2 6259 3771 168 114 6091 3657 5650 3022 174 122 5482 2908 0 0 3391 2330 54 49 100 100 100 100 9748 8390 1.666 .6 .53 .582 .548 1.197 32 236 .622 .99 70 2420 14150 39 46 62 69 0 5166 156 5010 .822 4140 3984 1.216 .727 -.282 -.461
3 16187 13186 171 109 16016 13077 14513 11692 182 123 14342 11583 0 0 10554 8783 134 78 100 100 98 96 29093 25925 1.225 .816 .808 .773 .781 1.275 52 400 .821 .99 90 2620 14120 35 44 81 90 0 18063 149 17914 1.118 16016 15867 .894 1.106 .162 .146
4 14413 10318 160 105 14253 10213 12202 8510 173 118 12042 8405 0 0 8517 6402 61 107 100 100 100 100 24466 20447 1.396 .717 .698 .724 .705 1.228 32 230 .724 .98 70 2820 14130 37 44 102 109 0 14134 144 13990 .982 11658 11514 1.019 .956 -.027 -.065
5 11202 8786 161 102 11041 8684 11387 8801 198 136 11226 8699 0 0 7449 5815 441 406 92 92 92 88 19725 19925 1.271 .787 .775 .752 .812 1.465 52 412 .774 .95 90 3010 14130 36 45 120 129 0 12036 140 11896 1.077 12056 11916 .928 1.062 .108 .086
6 23230 18885 165 101 23065 18784 24714 19568 183 126 24549 19467 0 0 9439 9200 297 370 98 92 94 92 41849 44016 1.228 .814 .793 .724 .772 1.408 52 412 .838 .99 90 3220 14130 36 45 141 150 0 25870 138 25732 1.116 26805 26667 .896 1.086 .158 .119
7 17442 12917 170 106 17272 12811 16743 12063 177 115 16573 11957 0 0 9681 7659 48 40 100 100 100 100 30083 28530 1.348 .742 .721 .702 .727 1.262 52 332 .754 .99 80 3420 14140 38 46 162 170 0 17695 145 17549 1.016 16525 16379 .984 .988 .023 -.017
8 8800 6002 161 97 8639 5905 8469 5113 178 106 8308 5016 0 0 4783 3923 78 40 100 100 100 100 14544 13324 1.463 .684 .604 .653 .658 1.201 32 170 .72 .97 60 3610 14140 39 45 182 188 0 8222 133 8089 .936 7004 6871 1.068 .827 -.095 -.274
9 11767 9425 169 105 11598 9320 12930 10283 177 112 12761 10178 0 0 7006 6076 79 43 100 100 100 100 20918 22939 1.244 .804 .798 .788 .795 1.316 52 320 .819 .99 80 3820 14140 38 46 202 210 0 12911 144 12767 1.101 14086 13942 .908 1.093 .139 .128
10 18080 14628 161 107 17919 14521 17244 14124 290 183 17083 14017 0 0 5373 4933 857 508 100 100 100 100 32440 31100 1.234 .81 .821 .799 .804 1.147 32 230 .817 .99 70 4020 14140 38 45 222 229 0 20038 147 19892 1.11 19348 19201 .901 1.124 .151 .169
11 427 219 154 102 273 117 298 173 161 107 144 71 0 0 332 128 42 33 100 75 93 59 390 215 2.333 .429 .493 .353 .43 2.346 32 160 .389 .92 60 4220 14140 39 45 243 249 -100 300 140 160 .587 237 97 1.703 .675 -.768 -.566
12 20818 17380 166 106 20652 17274 22546 18829 177 118 22380 18723 0 0 9830 8646 68 61 100 100 100 100 37926 41103 1.196 .836 .837 .781 .84 1.341 52 400 .848 .99 90 4430 14130 36 45 262 271 0 23808 145 23663 1.146 25793 25648 .873 1.146 .196 .197
13 19698 16791 169 102 19529 16689 20801 17362 176 111 20632 17260 0 0 8823 8330 55 40 100 100 100 100 36218 37892 1.17 .855 .837 .812 .838 1.319 52 320 .873 .99 80 4620 14140 38 46 282 290 0 23001 140 22862 1.171 23784 23644 .854 1.146 .227 .197
14 14030 10581 167 104 13863 10477 13991 9778 175 115 13824 9674 0 0 11096 8989 53 45 88 90 86 85 24340 23498 1.323 .756 .7 .701 .712 1.672 80 528 .778 .98 100 4830 14140 37 47 302 312 0 14495 142 14352 1.035 13395 13252 .966 .959 .05 -.061
15 10903 7543 169 116 10734 7427 9065 6383 186 125 8896 6267 0 0 5692 4681 66 47 100 100 100 100 18161 15163 1.445 .692 .704 .665 .664 1.248 32 236 .72 .96 70 5020 14150 39 46 322 329 0 10333 159 10174 .948 8744 8585 1.055 .965 -.077 -.051
16 12277 9278 164 103 12113 9175 12155 8256 173 110 11991 8153 0 0 6580 6608 52 44 100 100 100 100 21288 20144 1.32 .757 .68 .69 .674 1.24 32 236 .824 .97 70 5220 14150 39 46 342 349 0 12710 141 12568 1.038 11310 11168 .964 .931 .053 -.103
17 13762 11219 170 110 13592 11109 14092 11077 179 124 13922 10967 0 0 7215 6515 56 63 100 96 98 92 24701 24889 1.224 .817 .788 .745 .77 1.436 52 415 .837 .98 90 2230 14320 55 64 42 51 0 15368 151 15218 1.12 15174 15023 .893 1.079 .163 .11
18 14386 10995 179 120 14207 10875 15520 11265 194 131 15341 11145 0 0 7319 5824 124 70 100 100 100 100 25082 26486 1.306 .765 .726 .756 .738 1.275 52 420 .768 .97 90 2430 14330 56 65 62 71 0 15062 164 14897 1.049 15432 15267 .954 .995 .068 -.007
19 13880 10706 181 117 13699 10589 15380 11629 191 142 15199 11512 0 0 5620 4805 86 133 100 96 100 92 24288 26711 1.294 .773 .757 .712 .758 1.346 52 420 .778 .98 90 2630 14320 55 64 82 91 0 14666 160 14505 1.059 15930 15770 .944 1.038 .083 .053
20 14835 11710 160 105 14675 11605 15369 11349 169 116 15209 11244 0 0 8314 6072 56 52 98 100 98 100 26280 26453 1.265 .791 .739 .871 .868 1.476 52 340 .759 .97 80 2820 14350 59 67 102 110 0 16041 144 15897 1.083 15547 15403 .923 1.013 .115 .018

Total number of rows: 3840

Table truncated, full table size 902 Kbytes.




Supplementary data files not provided
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