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Sample GSM91155 Query DataSets for GSM91155
Status Public on Jan 07, 2006
Title Hly_vs_Un_T4_R2
Sample type RNA
 
Channel 1
Source name experimental sample
Organism Mus musculus
Characteristics experimental sample
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name experimental sample
Organism Mus musculus
Characteristics experimental sample
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Pathogen, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2002-02/25572.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 Jan 06, 2006
Last update date Sep 22, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) [email protected]
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 GPL3328
Series (1)
GSE3991 Listeria host responses

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 2239 2577 892 934 1347 1643 2417 2678 898 938 1525 1744 0 0 1129 1247 118 156 87 87 84 87 2990 3269 .82 1.22 1.144 1.037 1.155 2.457 32 224 1.413 .72 70 1920 7860 54 61 52 59 0 2863 1038 1826 1.355 2976 1938 .738 1.271 .439 .346
2 12946 12476 908 921 12038 11555 13579 12245 906 931 12671 11324 0 0 9558 7687 134 150 86 88 86 86 23593 23995 1.042 .96 .894 1.118 .912 3.381 52 344 .864 .89 90 2080 7860 53 62 67 76 0 13862 1023 12839 1.067 13606 12582 .938 .993 .093 -.01
3 8741 9934 911 920 7830 9014 8501 7568 917 940 7590 6648 0 0 4942 7236 115 138 92 97 92 96 16844 14238 .869 1.151 .876 1.148 1.07 2.669 80 396 1.317 .78 100 2240 7860 53 63 83 93 0 11038 1022 10016 1.279 8409 7387 .782 .973 .355 -.039
4 2133 3453 908 950 1225 2503 2141 3201 867 922 1233 2251 0 0 1184 2372 251 244 84 84 78 81 3728 3484 .489 2.043 1.826 1.486 1.76 3.134 32 206 2.331 .76 70 2380 7850 53 60 98 105 0 3837 1056 2781 2.27 3557 2501 .44 2.028 1.183 1.02
5 2437 3111 947 1006 1490 2105 2598 2813 936 1004 1651 1807 0 0 1363 1965 397 395 75 84 75 75 3595 3458 .708 1.413 1.094 1.12 1.034 2.901 32 226 1.474 .75 70 2520 7850 53 60 112 119 0 3457 1118 2339 1.57 3126 2008 .637 1.216 .651 .282
6 25581 23726 991 1092 24590 22634 26002 21352 1043 1141 25011 20260 0 0 17200 14546 240 259 88 98 86 98 47224 45271 1.086 .92 .81 1.106 .929 3.311 80 421 .859 .89 100 2690 7860 53 63 128 138 0 26362 1213 25149 1.023 23724 22511 .978 .9 .032 -.152
7 3271 5232 957 1120 2314 4112 2261 2455 924 1083 1304 1335 0 0 2880 5653 284 327 71 78 62 62 6426 2639 .563 1.777 1.024 1.416 1.433 2.688 32 188 1.971 .91 70 2800 7860 54 61 140 147 0 5813 1244 4569 1.974 2728 1483 .506 1.138 .981 .186
8 6577 5744 1010 1161 5567 4583 5981 5365 979 1133 4971 4204 0 0 3656 2939 229 273 93 93 93 87 10150 9175 1.215 .823 .846 .772 .82 2.048 32 210 .799 .89 70 2950 7850 53 60 155 162 0 6382 1290 5092 .915 5961 4671 1.093 .94 -.129 -.09
9 5006 4451 916 1049 4090 3402 1149 1556 721 819 233 507 0 0 8388 7019 442 516 42 50 32 40 7492 740 1.202 .832 2.176 1.307 1.18 3.267 52 230 .774 .73 80 3080 7860 54 62 168 176 -100 4946 1166 3780 .924 1729 563 1.082 2.418 -.114 1.274
10 1481 1661 144 166 1337 1495 970 1125 353 387 826 959 0 0 3508 3136 446 460 65 68 42 56 2832 1785 .894 1.118 1.161 1.319 1.203 2.88 80 366 .891 .7 100 3220 7840 51 61 181 191 -100 1846 184 1661 1.242 1250 1066 .805 1.29 .313 .367
11 791 736 121 151 670 585 130 162 134 162 9 11 0 0 2839 2225 64 69 15 23 11 19 1255 20 1.145 .873 1.222 .939 1 6.68 52 247 .774 .93 80 3380 7860 54 62 198 206 -100 818 168 650 .97 180 12 1.031 1.358 -.044 .442
12 423 639 118 141 305 498 120 144 131 157 2 3 0 0 829 1175 69 67 23 28 17 23 803 5 .612 1.633 1.5 1.822 1.669 3.982 52 246 1.351 .66 80 3520 7860 54 62 212 220 -100 710 157 553 1.814 160 3 .551 1.667 .859 .737
13 420 474 128 148 292 326 134 144 256 267 6 -4 0 0 897 916 452 365 11 17 7 13 618 2 .896 1.116 null 1.099 1.236 4.939 52 217 .883 .46 80 3670 7860 54 62 227 235 -100 527 164 362 1.24 160 null .806 null .311 null
14 2536 3275 120 145 2416 3130 436 743 213 221 316 598 0 0 3520 4957 442 303 47 55 42 49 5546 914 .772 1.296 1.892 1.302 1.278 3.995 156 773 1.486 .81 150 3820 7850 49 64 238 253 -100 3639 161 3478 1.439 826 664 .695 2.103 .526 1.072
15 987 956 119 140 868 816 131 157 208 231 12 17 0 0 4584 3569 332 313 9 15 5 15 1684 29 1.064 .94 1.417 1.511 1.068 5.916 52 201 .772 .94 80 3960 7860 54 62 256 264 -100 1062 156 907 1.045 174 19 .957 1.574 .063 .655
16 1616 1456 121 142 1495 1314 136 179 240 247 15 37 0 0 4229 3116 305 308 23 32 19 23 2809 52 1.138 .879 2.467 1.491 1.333 4.583 52 246 .567 .49 80 4100 7860 54 62 270 278 -100 1618 158 1460 .977 199 41 1.024 2.741 -.034 1.455
17 117 126 107 125 10 1 107 118 132 143 0 -7 0 0 39 42 146 115 0 0 0 0 11 -7 10 .1 null .993 1.333 3.764 52 261 .079 .14 80 4250 7860 54 62 285 293 -100 140 139 1 .111 131 null 9 null -3.17 null
18 100 113 103 113 -3 0 93 109 116 132 -10 -4 0 0 27 37 77 112 0 0 0 0 -3 -14 null null null .964 .893 3.255 52 259 3.212 .28 80 4400 7860 54 62 300 308 -100 126 126 0 null 121 null null null null null
19 116 122 100 113 16 9 106 104 116 124 6 -9 0 0 72 50 85 99 3 5 1 1 25 -3 1.778 .563 null 2.075 1.982 4.553 52 246 .841 .37 80 4540 7860 54 62 314 322 -100 136 126 10 .625 116 null 1.6 null -.678 null
20 1405 1651 96 112 1309 1539 110 147 121 129 14 35 0 0 4829 4480 90 106 21 30 21 23 2848 49 .851 1.176 2.5 1.25 .938 6.464 52 246 .865 .8 80 4690 7860 54 62 329 337 -100 1834 124 1710 1.306 163 39 .765 2.778 .386 1.474

Total number of rows: 42624

Table truncated, full table size 9744 Kbytes.




Supplementary data files not provided
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