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Sample GSM70935 Query DataSets for GSM70935
Status Public on Aug 20, 2005
Title Dauer MTC#2T6 (red, channel 2) vs. RefB-JW (green, channel 1)
Sample type RNA
 
Channel 1
Source name RefB-JW (green)
Organism Caenorhabditis elegans
Characteristics RefB-JW (green)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name Dauer MTC#2T6 (red)
Organism Caenorhabditis elegans
Characteristics Dauer MTC#2T6 (red)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: dauer, development
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11163.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 Aug 18, 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)
GSE3169 Global analysis of dauer gene expression 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 LOG_RAT2N_MEDIANs 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 LOG_RAT2N_MEDIAN of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized LOG_RAT2N_MEDIAN of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized LOG_RAT2N_MEDIAN 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 LOG_RAT2N_MEDIAN of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized LOG_RAT2N_MEDIAN 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 7550 3498 244 286 7306 3212 null null 255 357 null null null null null null null null 98 96 null null null null 2.275 .44 null null 2.234 null 80 441 .438 .98 null null null 63 73 64 74 0 4542 371 4171 .571 null null 1.752 null -.809 null
2 3002 4803 254 379 2748 4424 null null 274 463 null null null null null null null null 100 100 null null null null .621 1.61 null null .609 null 52 311 1.554 .96 null null null 63 72 82 91 0 6237 492 5745 2.091 null null .478 null 1.064 null
3 60315 14840 329 373 59986 14467 null null 394 557 null null null null null null null null 100 100 null null null null 4.146 .241 null null 3.797 null 12 94 .227 .96 null null null 63 68 95 100 0 19272 484 18788 .313 null null 3.193 null -1.675 null
4 4790 6184 249 294 4541 5890 null null 267 313 null null null null null null null null 100 100 null null null null .771 1.297 null null .768 null 52 387 1.233 .98 null null null 62 71 112 121 0 8031 381 7650 1.685 null null .594 null .752 null
5 12724 1082 244 244 12480 838 null null 256 257 null null null null null null null null 100 100 null null null null 14.893 .067 null null 15.543 null 52 316 .066 .97 null null null 62 70 130 138 0 1405 316 1089 .087 null null 11.46 null -3.519 null
6 1985 462 241 224 1744 238 null null 255 226 null null null null null null null null 96 100 null null null null 7.328 .136 null null 5.539 null 32 176 .108 .89 null null null 64 70 147 153 0 600 290 310 .178 null null 5.626 null -2.492 null
7 6616 4799 245 220 6371 4579 null null 253 222 null null null null null null null null 100 100 null null null null 1.391 .719 null null 1.412 null 80 546 .678 .98 null null null 59 70 160 171 0 6232 285 5947 .933 null null 1.071 null -.099 null
8 1061 593 244 223 817 370 null null 254 228 null null null null null null null null 100 100 null null null null 2.208 .453 null null 2.155 null 32 170 .445 .92 null null null 63 69 179 185 0 770 289 481 .589 null null 1.699 null -.764 null
9 29987 1269 260 248 29727 1021 null null 289 254 null null null null null null null null 100 100 null null null null 29.116 .034 null null 29.34 null 52 375 .033 .98 null null null 61 70 193 202 0 1648 322 1326 .045 null null 22.419 null -4.487 null
10 3045 2735 267 285 2778 2450 null null 308 306 null null null null null null null null 100 100 null null null null 1.134 .882 null null 1.099 null 32 230 .835 .97 null null null 62 69 209 216 0 3551 370 3181 1.145 null null .873 null .195 null
11 9928 6477 258 271 9670 6206 null null 272 282 null null null null null null null null 100 100 null null null null 1.558 .642 null null 1.549 null 80 546 .611 .98 null null null 59 70 224 235 0 8411 351 8060 .834 null null 1.2 null -.263 null
12 2635 2210 254 249 2381 1961 null null 263 255 null null null null null null null null 100 100 null null null null 1.214 .824 null null 1.206 null 52 284 .772 .96 null null null 62 70 242 250 0 2870 323 2547 1.07 null null .935 null .097 null
13 9682 5471 249 246 9433 5225 null null 257 250 null null null null null null null null 100 100 null null null null 1.805 .554 null null 1.801 null 52 301 .545 .98 null null null 63 71 258 266 0 7105 319 6786 .719 null null 1.39 null -.475 null
14 1351 790 260 265 1091 525 null null 274 268 null null null null null null null null 100 100 null null null null 2.078 .481 null null 2.031 null 52 300 .468 .93 null null null 62 70 274 282 0 1025 344 681 .624 null null 1.602 null -.68 null
15 1391 1544 263 267 1128 1277 null null 270 269 null null null null null null null null 100 100 null null null null .883 1.132 null null .891 null 52 374 1.022 .94 null null null 61 70 290 299 0 2005 346 1659 1.471 null null .68 null .557 null
16 1656 1069 274 275 1382 794 null null 289 281 null null null null null null null null 100 100 null null null null 1.741 .575 null null 1.761 null 52 284 .529 .93 null null null 62 70 307 315 0 1388 357 1031 .746 null null 1.34 null -.423 null
17 13133 27653 274 286 12859 27367 null null 286 290 null null null null null null null null 100 100 null null null null .47 2.128 null null .469 null 52 344 2.006 .98 null null null 61 70 321 330 0 35912 371 35541 2.764 null null .362 null 1.467 null
18 2070 3245 278 295 1792 2950 null null 293 298 null null null null null null null null 98 100 null null null null .607 1.646 null null .582 null 52 283 1.577 .95 null null null 62 70 338 346 0 4214 383 3831 2.138 null null .468 null 1.096 null
19 4650 4002 277 277 4373 3725 null null 282 280 null null null null null null null null 100 100 null null null null 1.174 .852 null null 1.21 null 52 344 .764 .96 null null null 61 70 352 361 0 5197 359 4838 1.106 null null .904 null .146 null
20 9796 1892 275 273 9521 1619 null null 283 280 null null null null null null null null 100 100 null null null null 5.881 .17 null null 5.912 null 80 430 .16 .98 null null null 60 70 369 379 0 2457 354 2103 .221 null null 4.527 null -2.179 null

Total number of rows: 21504

Table truncated, full table size 5232 Kbytes.




Supplementary data files not provided
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