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Sample GSM71126 Query DataSets for GSM71126
Status Public on Aug 20, 2005
Title L1 MTC#3T12 (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 L1 MTC#3T12 (red)
Organism Caenorhabditis elegans
Characteristics L1 MTC#3T12 (red)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Development, L1
Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13832.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 19, 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 GPL2754
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 12228 10865 229 323 11999 10542 13200 12552 244 334 12971 12229 0 0 3928 4498 154 104 100 100 100 100 22541 25200 1.138 .879 .943 .87 .932 .267 80 377 .884 .96 100 2080 18500 37 47 31 41 0 17030 506 16524 1.377 19675 19168 .726 1.478 .462 .563
2 3762 5647 226 333 3536 5314 3999 6494 232 334 3773 6161 0 0 1070 2260 72 99 100 100 99 100 8850 9934 .665 1.503 1.633 1.608 1.53 1.649 120 591 1.519 .96 130 2260 18510 36 49 47 60 0 8851 522 8329 2.356 10179 9657 .425 2.56 1.236 1.356
3 1428 1320 234 338 1194 982 1354 1291 240 343 1120 953 0 0 519 369 64 103 100 100 100 100 2176 2073 1.216 .822 .851 .894 .866 .353 52 316 .703 .86 90 2410 18500 37 46 64 73 0 2069 530 1539 1.289 2024 1494 .776 1.334 .366 .415
4 6150 5924 220 340 5930 5584 6038 5891 228 342 5818 5551 0 0 1192 811 67 114 100 100 100 100 11514 11369 1.062 .942 .954 .973 .939 .216 52 285 .868 .95 80 2570 18500 38 46 81 89 0 9286 533 8753 1.476 9234 8701 .678 1.496 .562 .581
5 11414 36945 200 323 11214 36622 12273 38005 204 331 12073 37682 0 0 2756 6141 49 103 100 100 100 100 47836 49755 .306 3.266 3.121 4.267 3.27 5.89 52 380 3.089 .98 90 2750 18500 37 46 98 107 0 57909 506 57403 5.119 59571 59065 .195 4.892 2.356 2.291
6 7997 6584 223 343 7774 6241 8731 8067 230 348 8508 7724 0 0 6269 3995 86 102 100 100 100 100 14015 16232 1.246 .803 .908 1.24 1.016 .687 12 90 .618 .93 50 2910 18490 38 43 116 121 0 10320 538 9782 1.258 12645 12107 .795 1.423 .332 .509
7 11190 4712 196 316 10994 4396 12371 5239 212 323 12175 4923 0 0 3358 1620 109 93 100 100 100 100 15390 17098 2.501 .4 .404 .4 .411 .1 80 519 .392 .96 110 3080 18500 36 47 130 141 0 7386 495 6890 .627 8212 7717 1.596 .634 -.674 -.658
8 4867 3264 194 313 4673 2951 4618 3215 216 330 4424 2902 0 0 2241 1331 133 139 100 100 100 100 7624 7326 1.584 .632 .656 .687 .614 .285 52 324 .55 .92 90 3230 18510 38 47 146 155 0 5116 491 4626 .99 5039 4549 1.01 1.028 -.015 .04
9 28217 1742 200 309 28017 1433 29043 1771 210 323 28843 1462 0 0 8375 524 79 125 100 98 100 95 29450 30305 19.551 .051 .051 .053 .05 .022 80 495 .049 .93 110 3400 18510 37 48 162 173 0 2730 484 2246 .08 2776 2292 12.473 .079 -3.641 -3.654
10 2939 2295 204 326 2735 1969 3066 2292 214 328 2862 1966 0 0 684 409 77 99 100 100 100 100 4704 4828 1.389 .72 .687 .748 .723 .163 52 315 .66 .95 90 3560 18500 37 46 179 188 0 3597 511 3086 1.128 3593 3082 .886 1.077 .174 .107
11 9477 5938 195 326 9282 5612 9922 6631 215 344 9727 6305 0 0 2939 2209 174 213 100 100 100 100 14894 16032 1.654 .605 .648 .587 .612 .152 80 502 .558 .95 110 3710 18490 35 46 193 204 0 9308 511 8797 .948 10394 9883 1.055 1.016 -.078 .023
12 2588 3173 199 328 2389 2845 2570 3190 215 343 2371 2862 0 0 517 483 94 120 100 100 100 100 5234 5233 .84 1.191 1.207 1.24 1.221 .289 52 375 1.07 .94 90 3890 18500 37 46 212 221 0 4974 514 4459 1.867 5000 4486 .536 1.892 .9 .92
13 278 403 187 322 91 81 192 352 192 332 5 30 0 0 408 219 49 99 28 31 12 18 172 35 1.123 .89 6 4.765 1.553 8.716 32 236 .622 .82 70 4050 18510 39 46 229 236 -50 632 505 127 1.395 552 47 .717 9.405 .48 3.233
14 1455 1286 182 313 1273 973 1123 1048 189 324 941 735 0 0 863 545 54 98 100 100 100 100 2246 1676 1.308 .764 .781 .835 .786 .295 52 364 .622 .87 90 4210 18510 38 47 244 253 0 2016 491 1525 1.198 1643 1152 .835 1.224 .261 .292
15 2951 2058 182 305 2769 1753 2644 1997 197 324 2462 1692 0 0 1364 757 143 100 100 100 100 100 4522 4154 1.58 .633 .687 .69 .663 .264 52 354 .557 .91 90 4370 18510 38 47 260 269 0 3226 478 2748 .992 3130 2652 1.008 1.077 -.011 .107
16 1675 1386 181 326 1494 1060 1446 1392 188 329 1265 1066 0 0 597 477 52 92 100 100 100 100 2554 2331 1.409 .71 .843 .731 .708 .277 52 362 .662 .9 90 4530 18510 38 47 276 285 0 2172 511 1661 1.112 2182 1671 .899 1.321 .153 .401
17 11811 19488 182 325 11629 19163 12263 19805 190 332 12081 19480 0 0 2802 3618 53 96 100 100 100 100 30792 31561 .607 1.648 1.612 1.836 1.634 .995 52 346 1.527 .96 90 4690 18500 37 46 292 301 0 30546 509 30037 2.583 31043 30534 .387 2.527 1.369 1.338
18 1053 1126 189 323 864 803 987 1093 205 337 798 770 0 0 222 303 88 102 100 98 100 98 1667 1568 1.076 .929 .965 .958 .923 .372 52 354 .826 .87 90 4850 18510 38 47 308 317 0 1765 506 1259 1.457 1713 1207 .686 1.512 .543 .597
19 3146 2578 184 330 2962 2248 3395 2669 201 334 3211 2339 0 0 910 708 98 92 100 100 100 100 5210 5550 1.318 .759 .728 .82 .754 .369 80 388 .729 .94 100 5020 18500 37 47 325 335 0 4041 517 3524 1.19 4184 3666 .841 1.142 .25 .191
20 5482 1757 183 322 5299 1435 6238 1962 193 327 6055 1640 0 0 1926 668 82 89 100 97 100 96 6734 7695 3.693 .271 .271 .26 .258 .099 80 448 .266 .95 110 5160 18500 36 47 338 349 0 2754 505 2249 .424 3075 2571 2.356 .425 -1.236 -1.236

Total number of rows: 21504

Table truncated, full table size 4868 Kbytes.




Supplementary data files not provided
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