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Sample GSM65030 Query DataSets for GSM65030
Status Public on Jul 22, 2005
Title New N2 mixed stage (red, channel 2) vs.L2 N2 T0new.2 (green, channel 1)
Sample type RNA
 
Channel 1
Source name L2 N2 T0new.2 (green, channel 1)
Organism Caenorhabditis elegans
Characteristics L2 N2 T0new.2 (green, channel 1)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name New N2 mixed stage (red, channel 2)
Organism Caenorhabditis elegans
Characteristics New N2 mixed stage (red, channel 2)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: C. elegans, Heat-shock
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11144.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 Jul 21, 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 GPL2653
Series (1)
GSE2974 Downstream targets of let-60 Ras 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 7742 4919 158 262 7584 4657 null null 164 267 null null null null null null null null 93 92 null null null null 1.629 .614 null null .603 null 120 554 .604 .96 null null null 89 101 63 75 0 5654 301 5353 .706 null null 1.417 null -.503 null
2 2438 3107 162 260 2276 2847 null null 171 272 null null null null null null null null 92 86 null null null null .799 1.251 null null 1.298 null 120 414 1.136 .93 null null null 89 101 80 92 0 3571 298 3273 1.438 null null .695 null .524 null
3 275 435 167 273 108 162 null null 176 287 null null null null null null null null 47 45 null null null null .667 1.5 null null 1.374 null 80 343 .852 .73 null null null 89 99 95 105 0 500 313 187 1.731 null null .578 null .792 null
4 951 1260 166 260 785 1000 null null 174 267 null null null null null null null null 80 85 null null null null .785 1.274 null null 1.227 null 120 499 1.182 .95 null null null 88 101 111 124 -100 1448 298 1150 1.465 null null .683 null .551 null
5 3016 1462 165 261 2851 1201 null null 188 290 null null null null null null null null 72 69 null null null null 2.374 .421 null null .885 null 120 492 .138 .49 null null null 88 101 129 142 0 1680 300 1380 .484 null null 2.066 null -1.047 null
6 1124 1603 166 274 958 1329 null null 171 278 null null null null null null null null 82 90 null null null null .721 1.387 null null 1.324 null 52 282 1.279 .92 null null null 90 99 146 155 0 1842 314 1528 1.595 null null .627 null .674 null
7 754 1261 161 274 593 987 null null 167 277 null null null null null null null null 62 71 null null null null .601 1.664 null null 1.793 null 120 471 1.462 .92 null null null 88 100 161 173 0 1449 314 1135 1.914 null null .522 null .937 null
8 1788 2067 163 269 1625 1798 null null 170 273 null null null null null null null null 77 92 null null null null .904 1.106 null null 1.107 null 80 373 1.009 .94 null null null 87 98 176 187 0 2375 309 2066 1.271 null null .787 null .346 null
9 1258 7139 168 265 1090 6874 null null 182 269 null null null null null null null null 71 91 null null null null .159 6.306 null null 6.34 null 156 582 5.293 .94 null null null 87 101 192 206 0 8205 304 7901 7.249 null null .138 null 2.858 null
10 1371 3070 170 264 1201 2806 null null 185 271 null null null null null null null null 68 91 null null null null .428 2.336 null null 2.603 null 120 400 1.988 .91 null null null 87 99 209 221 0 3528 303 3225 2.685 null null .372 null 1.425 null
11 10863 4679 170 264 10693 4415 null null 182 267 null null null null null null null null 97 95 null null null null 2.422 .413 null null .403 null 120 380 .405 .96 null null null 87 100 224 237 0 5378 303 5075 .475 null null 2.107 null -1.075 null
12 1873 2110 168 269 1705 1841 null null 196 300 null null null null null null null null 63 70 null null null null .926 1.08 null null 1.084 null 120 380 .959 .94 null null null 87 99 241 253 0 2425 309 2116 1.241 null null .806 null .312 null
13 830 1202 156 257 674 945 null null 168 261 null null null null null null null null 75 94 null null null null .713 1.402 null null 1.878 null 52 209 1.209 .83 null null null 89 97 258 266 0 1381 295 1086 1.611 null null .621 null .688 null
14 587 799 153 251 434 548 null null 159 255 null null null null null null null null 59 65 null null null null .792 1.263 null null 1.371 null 52 339 1.016 .87 null null null 88 97 272 281 0 918 288 630 1.452 null null .689 null .538 null
15 514 690 153 248 361 442 null null 158 253 null null null null null null null null 63 69 null null null null .817 1.224 null null 1.069 null 52 287 .877 .8 null null null 88 96 291 299 0 793 285 508 1.407 null null .711 null .493 null
16 1514 1660 168 259 1346 1401 null null 197 267 null null null null null null null null 78 82 null null null null .961 1.041 null null 1.214 null 52 292 .326 .63 null null null 88 97 305 314 0 1908 297 1611 1.197 null null .836 null .259 null
17 3787 2188 190 293 3597 1895 null null 194 296 null null null null null null null null 96 86 null null null null 1.898 .527 null null .556 null 52 293 .489 .9 null null null 87 96 322 331 0 2514 336 2178 .606 null null 1.652 null -.724 null
18 918 1079 177 291 741 788 null null 183 293 null null null null null null null null 67 68 null null null null .94 1.063 null null 1.291 null 80 301 .926 .89 null null null 88 98 338 348 0 1240 334 906 1.223 null null .818 null .29 null
19 1480 1960 167 249 1313 1711 null null 171 252 null null null null null null null null 86 87 null null null null .767 1.303 null null 1.254 null 80 283 1.217 .95 null null null 86 96 354 364 0 2252 286 1966 1.497 null null .668 null .582 null
20 1167 3615 162 254 1005 3361 null null 172 276 null null null null null null null null 76 79 null null null null .299 3.344 null null 4.035 null 120 389 2.338 .83 null null null 84 96 367 379 0 4155 291 3864 3.845 null null .26 null 1.943 null

Total number of rows: 21504

Table truncated, full table size 5238 Kbytes.




Supplementary data files not provided
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