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Sample GSM64906 Query DataSets for GSM64906
Status Public on Jul 21, 2005
Title N2 control #1 (red, channel 2) vs. testosterone 10e-09 (green, channel 1)
Sample type RNA
 
Channel 1
Source name testosterone 10e-09 (green)
Organism Caenorhabditis elegans
Characteristics testosterone 10e-09 (green)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name N2 control #1 (red)
Organism Caenorhabditis elegans
Characteristics N2 control #1 (red)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: C. elegans, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/10416.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 20, 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)
GSE2970 Caenorhabditis elegans as an environmental monitor using DNA microarray analysis.

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
1 734 784 69 182 665 602 null null 75 190 null null null null null null null null 88 71 null null null null 1.105 .905 null null .884 null 80 409 .939 .96 null null null 91 101 65 75 0 1005 233 772 1.161 null null .861 null .215 null
2 496 418 65 191 431 227 null null 69 192 null null null null null null null null 70 65 null null null null 1.899 .527 null null .533 null 80 436 .534 .86 null null null 89 100 80 91 0 535 244 291 .675 null null 1.481 null -.567 null
3 169 273 64 194 105 79 null null 68 197 null null null null null null null null 59 46 null null null null 1.329 .752 null null 1.051 null 52 314 .602 .51 null null null 89 98 96 105 0 350 248 102 .971 null null 1.029 null -.042 null
4 1249 683 63 196 1186 487 null null 66 201 null null null null null null null null 96 66 null null null null 2.435 .411 null null .447 null 80 441 .416 .94 null null null 88 99 111 122 0 875 251 624 .526 null null 1.901 null -.926 null
5 627 976 61 200 566 776 null null 64 203 null null null null null null null null 78 62 null null null null .729 1.371 null null 1.291 null 120 456 1.45 .95 null null null 88 100 128 140 0 1251 256 995 1.758 null null .569 null .814 null
6 119 269 65 200 54 69 null null 69 201 null null null null null null null null 61 38 null null null null .783 1.278 null null 2.933 null 52 241 .747 .39 null null null 89 97 144 152 0 344 256 88 1.63 null null .614 null .705 null
7 1258 1412 71 191 1187 1221 null null 77 199 null null null null null null null null 95 77 null null null null .972 1.029 null null .988 null 80 521 1.08 .96 null null null 87 98 160 171 0 1810 244 1566 1.319 null null .758 null .4 null
8 314 313 75 192 239 121 null null 79 198 null null null null null null null null 91 45 null null null null 1.975 .506 null null .82 null 80 340 .404 .6 null null null 88 98 180 190 0 401 246 155 .649 null null 1.542 null -.625 null
9 5386 2798 75 195 5311 2603 null null 80 200 null null null null null null null null 90 73 null null null null 2.04 .49 null null .483 null 120 550 .502 .97 null null null 85 98 191 204 0 3587 250 3337 .628 null null 1.592 null -.67 null
10 473 506 78 206 395 300 null null 90 207 null null null null null null null null 75 73 null null null null 1.317 .759 null null .909 null 52 318 .693 .84 null null null 86 95 209 218 0 648 264 384 .972 null null 1.029 null -.041 null
11 2305 1184 78 199 2227 985 null null 85 200 null null null null null null null null 98 87 null null null null 2.261 .442 null null .427 null 80 466 .475 .96 null null null 85 96 224 235 0 1517 255 1262 .567 null null 1.765 null -.819 null
12 317 383 75 197 242 186 null null 78 203 null null null null null null null null 78 65 null null null null 1.301 .769 null null .826 null 52 323 .702 .75 null null null 87 96 241 250 0 491 252 239 .988 null null 1.013 null -.018 null
13 1356 987 71 206 1285 781 null null 73 207 null null null null null null null null 82 56 null null null null 1.645 .608 null null .593 null 80 485 .64 .94 null null null 85 96 257 268 0 1265 264 1001 .779 null null 1.284 null -.36 null
14 241 365 72 193 169 172 null null 73 201 null null null null null null null null 73 59 null null null null .983 1.018 null null 1.033 null 52 334 .812 .69 null null null 86 95 274 283 0 467 247 220 1.302 null null .768 null .38 null
15 294 418 75 189 219 229 null null 78 200 null null null null null null null null 69 78 null null null null .956 1.046 null null 1.105 null 52 334 .804 .78 null null null 86 95 290 299 0 535 242 293 1.338 null null .747 null .42 null
16 531 487 84 188 447 299 null null 88 196 null null null null null null null null 83 68 null null null null 1.495 .669 null null .809 null 80 444 .616 .83 null null null 85 96 305 316 0 624 241 383 .857 null null 1.167 null -.223 null
17 2544 1478 92 199 2452 1279 null null 95 204 null null null null null null null null 92 85 null null null null 1.917 .522 null null .542 null 80 437 .537 .96 null null null 84 95 321 332 0 1894 255 1639 .668 null null 1.496 null -.581 null
18 298 369 90 196 208 173 null null 95 202 null null null null null null null null 65 61 null null null null 1.202 .832 null null .947 null 80 401 .697 .76 null null null 85 95 338 348 0 473 251 222 1.067 null null .937 null .094 null
19 985 720 85 194 900 526 null null 91 199 null null null null null null null null 95 71 null null null null 1.711 .584 null null .61 null 80 407 .61 .92 null null null 85 96 353 364 0 923 248 675 .75 null null 1.333 null -.415 null
20 2887 1581 89 194 2798 1387 null null 94 202 null null null null null null null null 79 56 null null null null 2.017 .496 null null .512 null 120 513 .509 .96 null null null 84 96 369 381 0 2026 248 1778 .635 null null 1.574 null -.654 null

Total number of rows: 21504

Table truncated, full table size 5067 Kbytes.




Supplementary data files not provided
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