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Sample GSM69762 Query DataSets for GSM69762
Status Public on Aug 13, 2005
Title "mutant sorted touch cell (red, channel 2) vs. wt sorted touch cell (repeat #2) (green, channel 1)"
Sample type RNA
 
Channel 1
Source name wt sorted touch cell (green)
Organism Caenorhabditis elegans
Characteristics wt sorted touch cell (green)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name mutant sorted touch cell (red)
Organism Caenorhabditis elegans
Characteristics mutant sorted touch cell (red)
Extracted molecule total RNA
Label Cy5
 
 
Description Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/17042.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 Aug 12, 2005
Last update date Sep 22, 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 GPL2646
Series (1)
GSE3121 Identification of genes expressed in C. elegans touch receptor neurons

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
1 129 121 87 123 42 -2 129 122 90 126 42 -1 0 0 40 33 26 31 60 16 40 2 40 41 null null null 1.004 .53 1.419 120 586 .083 .09 120 2400 16040 142 154 226 238 0 173 176 -3 null 175 -1 null null null null
2 149 136 85 115 64 21 154 130 89 118 69 15 0 0 40 33 27 29 77 37 65 10 85 84 3.048 .328 .217 1.58 .554 3.871 80 356 .145 .18 100 2570 16040 143 153 244 254 0 195 165 30 .47 186 21 2.128 .311 -1.09 -1.684
3 156 127 85 117 71 10 157 127 88 120 72 10 0 0 31 27 26 31 90 23 75 1 81 82 7.1 .141 .139 .962 .419 3.339 52 305 .072 .09 90 2710 16050 144 153 258 267 0 182 168 14 .202 182 14 4.958 .199 -2.31 -2.33
4 163 130 84 124 79 6 161 128 87 125 77 4 0 0 36 37 22 32 96 25 88 7 85 81 13.167 .076 .052 .504 .345 .522 52 349 .047 .05 90 2880 16050 144 153 275 284 0 186 178 9 .109 183 6 9.195 .074 -3.201 -3.749
5 158 146 85 125 73 21 158 144 89 128 73 19 0 0 37 36 26 32 90 38 73 13 94 92 3.476 .288 .26 .717 .563 .638 52 363 .153 .18 90 3050 16050 144 153 292 301 0 209 179 30 .412 206 27 2.428 .373 -1.28 -1.424
6 133 166 86 126 47 40 111 151 89 131 25 25 0 0 54 61 19 33 57 46 40 28 87 50 1.175 .851 1 5.183 1.179 11.59 52 260 .343 .3 80 3220 16080 148 156 310 318 0 238 180 57 1.219 216 36 .821 1.432 .285 .518
7 145 151 87 133 58 18 148 144 89 135 61 11 0 0 45 38 22 35 76 26 63 6 76 72 3.222 .31 .18 1.427 .5 3.985 120 498 .172 .19 120 3370 16050 143 155 323 335 0 216 190 26 .444 206 16 2.25 .258 -1.17 -1.953
8 148 174 87 126 61 48 143 170 89 129 56 44 0 0 49 57 19 32 81 61 68 30 109 100 1.271 .787 .786 3.07 1 9.461 80 340 .476 .42 100 3540 16050 144 154 341 351 0 249 180 69 1.127 243 63 .887 1.125 .172 .17
9 149 135 87 123 62 12 148 137 116 133 61 14 0 0 43 38 243 79 0 5 0 0 74 75 5.167 .194 .23 .934 .494 1.571 120 464 .167 .2 120 3700 16050 143 155 356 368 0 193 176 17 .277 196 20 3.608 .329 -1.851 -1.605
10 166 145 84 121 82 24 162 144 86 124 78 23 0 0 46 35 18 30 95 41 85 16 106 101 3.417 .293 .295 .978 .389 2.661 80 343 .237 .31 110 3860 16050 143 154 372 383 0 208 173 34 .419 206 33 2.386 .422 -1.255 -1.244
11 147 135 85 122 62 13 146 131 89 127 61 9 0 0 48 33 25 31 75 28 55 10 75 70 4.769 .21 .148 1.349 .513 3.776 120 457 .101 .12 120 4010 16040 142 154 387 399 0 193 175 19 .3 188 13 3.331 .211 -1.736 -2.243
12 155 145 85 122 70 23 153 141 88 126 68 19 0 0 35 33 22 33 92 31 80 11 93 87 3.043 .329 .279 2.419 .426 11.594 80 410 .135 .19 110 4170 16050 143 154 403 414 0 208 175 33 .471 202 27 2.125 .4 -1.088 -1.322
13 161 171 85 124 76 47 158 171 88 126 73 47 0 0 46 46 22 37 86 57 78 23 123 120 1.617 .618 .644 .976 .625 1.188 80 385 .403 .44 100 4320 16060 145 155 419 429 0 245 178 67 .886 245 67 1.129 .922 -.175 -.117
14 136 130 86 124 50 6 136 128 89 129 50 4 0 0 42 33 25 42 65 13 48 0 56 54 8.333 .12 .08 1.909 .38 5.679 120 520 .153 .17 120 4490 16040 142 154 435 447 0 186 178 9 .172 183 6 5.82 .115 -2.541 -3.126
15 131 127 87 122 44 5 137 121 90 128 50 -1 0 0 42 36 27 39 62 14 45 2 49 49 8.8 .114 null 1.945 .487 4.452 120 520 .055 .05 120 4650 16040 142 154 451 463 0 182 175 7 .163 173 -1 6.145 null -2.62 null
16 125 145 89 119 36 26 121 141 96 124 32 22 0 0 45 41 31 32 50 38 32 17 62 54 1.385 .722 .688 2.684 .785 5.728 52 241 .093 .1 80 4820 16010 141 149 470 478 0 208 170 37 1.034 202 32 .967 .984 .049 -.023
17 326 234 85 127 241 107 345 234 89 130 260 107 0 0 154 76 24 34 85 79 80 68 348 367 2.252 .444 .412 .814 .446 1.417 120 516 .394 .78 130 4980 16060 143 156 483 496 0 335 182 153 .636 335 153 1.573 .589 -.653 -.763
18 162 142 82 132 80 10 160 143 84 133 78 11 0 0 36 41 24 35 96 26 84 5 90 89 8 .125 .141 .852 .403 2.04 52 249 .138 .16 90 5130 16060 145 154 500 509 0 203 189 14 .179 205 16 5.587 .202 -2.482 -2.308
19 140 143 85 135 55 8 141 139 87 138 56 4 0 0 42 38 26 36 70 19 53 5 63 60 6.875 .145 .071 1.902 .597 4.193 120 470 .108 .13 120 5290 16040 142 154 515 527 0 205 193 11 .208 199 6 4.801 .102 -2.263 -3.289
20 159 154 86 136 73 18 163 149 89 141 77 13 0 0 36 38 25 39 90 23 78 3 91 90 4.056 .247 .169 1.073 .315 2.365 80 367 .066 .07 110 5450 16050 143 154 531 542 0 221 195 26 .353 213 19 2.832 .242 -1.502 -2.048

Total number of rows: 21504

Table truncated, full table size 4443 Kbytes.




Supplementary data files not provided
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