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Sample GSM94445 Query DataSets for GSM94445
Status Public on Feb 01, 2006
Title N2-I (starting line) (red, channel 2) vs. MA59-I (no selection) (green, channel 1)
Sample type RNA
 
Channel 1
Source name MA59-I (no selection) (green)
Organism Caenorhabditis elegans
Characteristics MA59-I (no selection) (green)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name N2-I (starting line) (red)
Organism Caenorhabditis elegans
Characteristics N2-I (starting line) (red)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: evolution, Thomas Strains
Image: http://smd.stanford.edu/MicroArray/gifs/1999-12/1583.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 Jan 30, 2006
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 GPL3098
Series (1)
GSE4123 The transcriptional consequences of mutation and natural selection in Caenorhabditis elegans

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 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
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

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
1 969 799 189 105 780 694 null null 193 108 null null null null null null null null 67 55 null null null null 1.124 .89 null null .892 null 120 535 .683 .728 null null null 60 72 49 61 0 928 122 806 1.034 null null .967 null .048 null
2 574 433 182 116 392 317 null null 186 119 null null null null null null null null 60 49 null null null null 1.237 .809 null null .861 null 120 378 .619 .729 null null null 60 72 65 77 0 503 135 368 .94 null null 1.064 null -.09 null
3 457 335 185 118 272 217 null null 191 122 null null null null null null null null 50 35 null null null null 1.253 .798 null null .963 null 120 378 .478 .514 null null null 60 72 81 93 0 389 137 252 .927 null null 1.079 null -.109 null
4 1332 1126 188 120 1144 1006 null null 193 123 null null null null null null null null 60 49 null null null null 1.137 .879 null null .787 null 120 370 .701 .779 null null null 60 72 97 109 0 1308 139 1169 1.022 null null .979 null .031 null
5 1730 1804 191 120 1539 1684 null null 198 125 null null null null null null null null 68 60 null null null null .914 1.094 null null 1.065 null 120 386 .88 .798 null null null 59 71 113 125 0 2096 139 1957 1.271 null null .786 null .347 null
6 431 265 197 120 234 145 null null 201 127 null null null null null null null null 44 33 null null null null 1.614 .62 null null .636 null 120 378 .484 .645 null null null 59 71 129 141 0 308 139 168 .72 null null 1.389 null -.474 null
7 3127 2987 200 121 2927 2866 null null 206 128 null null null null null null null null 97 96 null null null null 1.021 .979 null null 1.044 null 120 420 .895 .845 null null null 58 71 144 157 0 3471 141 3330 1.138 null null .879 null .186 null
8 864 865 198 127 666 738 null null 205 134 null null null null null null null null 60 65 null null null null .902 1.108 null null 1.17 null 120 378 .755 .714 null null null 59 71 161 173 0 1005 148 858 1.288 null null .777 null .365 null
9 336 368 192 128 144 240 null null 197 140 null null null null null null null null 44 45 null null null null .6 1.667 null null 1.625 null 120 378 .92 .568 null null null 59 71 177 189 0 428 149 279 1.937 null null .516 null .954 null
10 1074 1267 203 124 871 1143 null null 206 137 null null null null null null null null 80 85 null null null null .762 1.312 null null 1.354 null 120 378 .903 .715 null null null 59 71 193 205 0 1472 144 1328 1.525 null null .656 null .609 null
11 683 498 225 129 458 369 null null 247 145 null null null null null null null null 88 85 null null null null 1.241 .806 null null .65 null 120 378 .667 .666 null null null 59 71 209 221 0 579 150 429 .936 null null 1.068 null -.095 null
12 4258 3292 212 149 4046 3143 null null 228 165 null null null null null null null null 70 72 null null null null 1.287 .777 null null .834 null 120 378 .665 .819 null null null 59 71 225 237 0 3825 173 3652 .903 null null 1.108 null -.148 null
13 1556 1776 203 147 1353 1629 null null 212 157 null null null null null null null null 60 75 null null null null .831 1.204 null null 1.361 null 120 378 .93 .832 null null null 59 71 241 253 0 2064 171 1893 1.399 null null .715 null .484 null
14 451 304 201 146 250 158 null null 207 147 null null null null null null null null 45 43 null null null null 1.582 .632 null null 1.031 null 120 378 .275 .389 null null null 59 71 257 269 0 353 170 184 .734 null null 1.362 null -.445 null
15 468 259 201 142 267 117 null null 206 146 null null null null null null null null 52 51 null null null null 2.282 .438 null null .5 null 120 378 .275 .565 null null null 59 71 273 285 0 301 165 136 .509 null null 1.964 null -.974 null
16 589 377 212 138 377 239 null null 214 145 null null null null null null null null 62 56 null null null null 1.577 .634 null null .738 null 120 370 .429 .655 null null null 59 71 289 301 -100 438 160 278 .737 null null 1.357 null -.441 null
17 1657 1463 210 136 1447 1327 null null 212 140 null null null null null null null null 76 66 null null null null 1.09 .917 null null .795 null 120 386 .726 .762 null null null 58 70 305 317 0 1700 158 1542 1.066 null null .938 null .092 null
18 603 360 203 131 400 229 null null 208 137 null null null null null null null null 68 61 null null null null 1.747 .573 null null .658 null 120 378 .44 .672 null null null 58 70 321 333 0 418 152 266 .665 null null 1.503 null -.588 null
19 939 844 217 141 722 703 null null 224 145 null null null null null null null null 47 44 null null null null 1.027 .974 null null 1.051 null 120 378 .752 .74 null null null 58 70 337 349 0 981 164 817 1.131 null null .884 null .178 null
20 2616 2496 231 146 2385 2350 null null 235 157 null null null null null null null null 78 61 null null null null 1.015 .985 null null .751 null 120 378 .805 .793 null null null 58 70 353 365 0 2900 170 2731 1.145 null null .873 null .195 null

Total number of rows: 21120

Table truncated, full table size 5106 Kbytes.




Supplementary data files not provided
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