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Sample GSM140628 Query DataSets for GSM140628
Status Public on Oct 18, 2006
Title NGM versus CeMM growth #1
Sample type RNA
 
Channel 1
Source name NGM grown mixed stage animals
Organism Caenorhabditis elegans
Characteristics Plate Grown
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name CeMM grown mixed stage animals
Organism Caenorhabditis elegans
Characteristics Culture Grown
Extracted molecule total RNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol not provided
Description Simple annotation: C. elegans, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/33635.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 Oct 17, 2006
Last update date Oct 17, 2006
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 GPL3411
Series (1)
GSE6057 NGM versus CeMM growth

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
1 143 130 69 125 74 5 98 124 79 139 29 -1 0 0 163 49 89 166 19 0 10 0 79 28 14.8 .068 null 1 1 1 120 525 1 .2 120 2410 18660 47 59 76 88 -50 3250 3125 125 1.689 3100 null .592 null .756 null
2 197 133 70 125 127 8 110 123 89 142 40 -2 0 0 332 74 152 188 13 3 7 1 135 38 15.875 .063 null 1 1 1 120 386 1 .08 120 2570 18660 47 59 92 104 -50 3325 3125 200 1.575 3075 null .635 null .655 null
3 118 138 73 133 45 5 86 127 124 143 13 -6 0 0 107 71 384 75 2 8 0 3 50 7 9 .111 null 1 1 1 120 338 1 .34 120 2730 18660 47 59 108 120 -50 3450 3325 125 2.778 3175 null .36 null 1.474 null
4 153 143 76 132 77 11 115 128 252 156 39 -4 0 0 187 82 2144 184 0 5 0 1 88 35 7 .143 null 1 1 1 120 407 1 .19 120 2860 18650 46 58 121 133 0 3575 3300 275 3.571 3200 null .28 null 1.837 null
5 412 130 75 131 337 -1 336 130 139 141 261 -1 0 0 417 54 569 66 12 8 4 0 336 260 null null null 1 1 1 120 424 1 .04 120 3060 18660 47 59 141 153 0 3250 3275 -25 null 3250 null null null null null
6 125 129 76 132 49 -3 91 113 144 137 15 -19 0 0 88 59 594 59 0 8 0 2 46 -4 null null null 1 1 1 120 376 1 .04 120 3210 18660 47 59 156 168 -50 3225 3300 -75 null 2825 null null null null null
7 238 117 70 118 168 -1 185 113 86 121 115 -5 0 0 368 42 74 46 65 13 36 1 167 110 null null null 1 1 1 120 440 1 .04 120 3370 18660 47 59 172 184 0 2925 2950 -25 null 2825 null null null null null
8 874 325 75 113 799 212 298 147 83 114 223 34 0 0 1988 989 37 38 95 45 85 23 1011 257 3.769 .265 .152 1 1 1 120 414 1 .45 120 3570 18660 47 59 192 204 0 8125 2825 5300 6.633 3675 850 .151 3.812 2.73 1.93
9 3704 337 76 112 3628 225 2428 176 87 114 2352 64 0 0 5326 525 67 39 95 65 89 40 3853 2416 16.124 .062 .027 1 1 1 120 352 1 .7 120 3700 18660 47 59 205 217 0 8425 2800 5625 1.55 4400 1600 .645 .68 .633 -.556
10 206 117 76 115 130 2 160 115 95 118 84 0 0 0 168 43 83 41 50 16 25 3 132 84 65 .015 null 1 1 1 120 378 1 .09 120 3860 18660 47 59 221 233 -50 2925 2875 50 .385 2875 0 2.6 null -1.379 null
11 4258 1534 80 111 4178 1423 1000 137 99 117 920 26 2 0 12936 6864 71 41 86 44 78 27 5601 946 2.936 .341 .028 1 1 1 120 400 1 .66 120 4020 18650 46 58 237 249 0 38350 2775 35575 8.515 3425 650 .117 .707 3.09 -.501
12 98 117 72 105 26 12 87 114 78 110 15 9 0 0 50 41 26 37 33 23 15 7 38 24 2.167 .462 .6 1 1 1 120 381 1 .06 120 4180 18660 47 59 253 265 -50 2925 2625 300 11.538 2850 225 .087 15 3.528 3.907
13 128 106 69 105 59 1 113 101 76 109 44 -4 0 0 60 35 25 38 72 14 43 2 60 40 59 .017 null 1 1 1 120 386 -1 -1 120 4340 18670 48 60 269 281 0 2650 2625 25 .424 2525 null 2.36 null -1.239 null
14 192 117 78 106 114 11 158 112 88 111 80 6 0 0 104 38 38 40 67 20 54 5 125 86 10.364 .096 .075 1 1 1 120 427 1 .03 120 4520 18650 46 58 287 299 0 2925 2650 275 2.412 2800 150 .415 1.875 1.27 .907
15 223 116 81 108 142 8 197 111 93 115 116 3 0 0 178 43 40 40 85 19 71 5 150 119 17.75 .056 .026 1 1 1 120 321 1 .04 120 4660 18670 48 60 301 313 0 2900 2700 200 1.408 2775 75 .71 .647 .494 -.629
16 268 125 75 109 193 16 254 124 80 113 179 15 0 0 224 47 32 36 83 28 80 8 209 194 12.063 .083 .084 1 1 1 120 378 1 .35 120 4810 18660 47 59 316 328 0 3125 2725 400 2.073 3100 375 .483 2.095 1.051 1.067
17 1164 132 76 112 1088 20 1021 128 83 116 945 16 0 0 911 45 39 39 84 28 79 8 1108 961 54.4 .018 .017 1 1 1 120 412 1 .17 120 4980 18660 47 59 333 345 0 3300 2800 500 .46 3200 400 2.176 .423 -1.122 -1.24
18 1034 310 92 119 942 191 766 128 234 189 674 9 0 0 1666 844 1025 572 15 5 5 4 1133 683 4.932 .203 .013 1 1 1 120 397 1 .89 120 5150 18660 47 59 350 362 0 7750 2975 4775 5.069 3200 225 .197 .334 2.342 -1.583
19 260 121 86 116 174 5 247 120 240 193 161 4 0 0 124 38 1088 607 0 0 0 0 179 165 34.8 .029 .025 1 1 1 120 352 1 .93 120 5310 18670 48 60 366 378 0 3025 2900 125 .718 3000 100 1.392 .621 -.477 -.687
20 201 115 78 116 123 -1 127 114 221 140 49 -2 0 0 234 36 1791 230 0 0 0 0 122 47 null null null 1 1 1 120 381 1 .08 120 5470 18660 47 59 382 394 -50 2875 2900 -25 null 2850 null null null null null

Total number of rows: 21504

Table truncated, full table size 4487 Kbytes.




Supplementary data files not provided
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