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Sample GSM94457 Query DataSets for GSM94457
Status Public on Feb 01, 2006
Title "MA41-1(B) (red, channel 2) vs. MA83-1(A) (green, channel 1)"
Sample type RNA
 
Channel 1
Source name MA83-1(A) (green)
Organism Caenorhabditis elegans
Characteristics MA83-1(A) (green)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name MA41-1(B) (red)
Organism Caenorhabditis elegans
Characteristics MA41-1(B) (red)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: C. elegans, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16495.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 GPL2646
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 3773 2828 139 308 3634 2520 1628 1750 145 317 1489 1442 0 0 3618 2494 56 74 92 87 89 80 6154 2931 1.442 .693 .968 1.85 .659 9.174 120 624 .663 .96 130 1200 18590 76 89 45 58 0 1531 167 1364 .375 947 780 2.665 .524 -1.414 -.932
2 2041 1749 141 313 1900 1436 2275 1892 147 321 2134 1579 0 0 1389 1104 56 74 89 86 85 82 3336 3713 1.323 .756 .74 1.202 .806 2.021 120 483 .727 .94 130 1380 18600 77 90 63 76 0 947 169 777 .409 1024 855 2.445 .4 -1.29 -1.32
3 551 1150 134 312 417 838 416 1052 144 316 282 740 0 0 382 627 54 73 82 96 71 87 1255 1022 .498 2.01 2.624 4.787 2.259 11.419 80 320 1.636 .89 100 1540 18600 79 89 81 91 0 622 169 454 1.088 569 400 .919 1.42 .121 .506
4 1797 2319 134 308 1663 2011 655 1402 142 312 521 1094 0 0 1806 2057 52 68 79 86 75 75 3674 1615 .827 1.209 2.1 1.954 1.219 2.873 120 442 1.118 .96 120 1700 18600 78 90 96 108 0 1255 167 1088 .654 759 592 1.528 1.136 -.612 .184
5 3305 7740 134 325 3171 7415 1901 5367 246 487 1767 5042 0 0 3174 7071 924 1353 57 65 50 58 10586 6809 .428 2.338 2.853 4.347 2.375 9.778 120 465 2.145 .95 120 1870 18600 78 90 113 125 0 4189 176 4013 1.266 2905 2729 .79 1.544 .34 .627
6 543 975 134 298 409 677 301 694 351 642 167 396 0 0 497 636 1318 1934 5 3 0 0 1086 563 .604 1.655 2.371 5.254 1.834 11.8 52 225 1.254 .89 80 2030 18580 78 86 131 139 0 528 161 366 .896 376 214 1.116 1.283 -.159 .36
7 2464 2165 132 287 2332 1878 2844 2456 141 294 2712 2169 0 0 1669 1356 57 68 91 94 89 90 4210 4881 1.242 .805 .8 1.149 .763 2.11 156 591 .773 .95 140 2180 18590 76 90 143 157 0 1172 155 1016 .436 1329 1174 2.294 .433 -1.198 -1.208
8 932 1511 128 288 804 1223 1028 1556 137 295 900 1268 0 0 629 931 54 68 81 87 76 82 2027 2168 .657 1.521 1.409 3.053 1.554 7.25 120 367 1.36 .91 130 2350 18590 76 89 160 173 0 818 156 662 .823 842 686 1.215 .762 -.281 -.391
9 12640 14524 132 283 12508 14241 7053 5413 139 289 6921 5130 0 0 11840 14885 54 64 90 95 86 91 26749 12051 .878 1.139 .741 2.568 1.1 8.822 208 831 1.163 .96 170 2500 18590 74 91 173 190 0 7860 153 7707 .616 2930 2776 1.623 .401 -.699 -1.318
10 1252 2203 140 290 1112 1913 1446 2654 145 291 1306 2364 0 0 715 1110 58 63 91 98 86 97 3025 3670 .581 1.72 1.81 2.363 1.766 2.412 120 418 1.557 .94 130 2680 18590 76 89 193 206 0 1192 157 1035 .931 1436 1279 1.074 .98 -.103 -.03
11 7910 5573 133 285 7777 5288 8842 6576 140 288 8709 6291 0 0 5279 3872 54 65 93 94 86 92 13065 15000 1.471 .68 .722 1.564 .709 4.249 156 571 .68 .97 150 2840 18590 75 90 208 223 0 3016 154 2862 .368 3559 3405 2.717 .391 -1.442 -1.355
12 1057 1626 132 277 925 1349 1181 1873 138 281 1049 1596 0 0 577 804 52 67 98 99 90 94 2274 2645 .686 1.458 1.521 1.995 1.426 3.392 120 411 1.324 .93 130 2990 18590 76 89 224 237 0 880 150 730 .789 1014 864 1.267 .823 -.341 -.28
13 2421 2763 130 283 2291 2480 706 1173 138 285 576 890 0 0 2858 3041 53 62 77 82 72 74 4771 1466 .924 1.082 1.545 2.12 1.012 3.845 120 390 1.015 .95 120 3150 18600 78 90 241 253 0 1495 153 1342 .586 635 482 1.707 .836 -.771 -.258
14 753 1286 129 291 624 995 699 1344 137 295 570 1053 0 0 416 546 52 65 93 98 88 93 1619 1623 .627 1.595 1.847 2.253 1.568 2.42 80 383 1.385 .92 110 3310 18590 77 88 257 268 0 696 157 538 .863 727 570 1.159 1 -.213 0
15 509 983 129 296 380 687 345 784 136 296 216 488 0 0 445 680 53 66 69 73 57 69 1067 704 .553 1.808 2.259 2.781 1.723 2.951 120 496 1.457 .89 120 3470 18590 77 89 273 285 0 532 160 372 .978 424 264 1.022 1.223 -.031 .29
16 1080 1987 133 293 947 1694 1027 2015 143 297 894 1722 0 0 650 987 80 83 91 98 87 98 2641 2616 .559 1.789 1.926 2.816 1.854 3.719 80 411 1.56 .92 110 3640 18590 77 88 290 301 0 1075 159 917 .968 1091 932 1.033 1.042 -.047 .06
17 4931 7648 132 287 4799 7361 4777 8058 141 289 4645 7771 0 0 3087 4860 51 62 100 100 100 100 12160 12416 .652 1.534 1.673 1.677 1.538 .93 80 408 1.491 .96 110 3790 18590 77 88 305 316 0 4139 155 3984 .83 4361 4206 1.205 .905 -.269 -.143
18 714 1352 131 278 583 1074 564 1229 140 279 433 951 0 0 597 988 50 68 72 79 65 75 1657 1384 .543 1.842 2.196 2.708 1.734 3.57 120 463 1.618 .93 120 3970 18580 76 88 323 335 0 732 150 581 .997 665 515 1.003 1.189 -.004 .249
19 1546 1664 131 263 1415 1401 1103 1211 137 269 972 948 0 0 1425 1429 49 66 80 77 75 71 2816 1920 1.01 .99 .975 1.494 .928 1.764 120 413 .915 .92 120 4110 18580 76 88 337 349 0 901 142 758 .536 655 513 1.866 .528 -.9 -.922
20 4186 5056 129 282 4057 4774 3666 3595 135 286 3537 3313 0 0 3310 4210 51 64 85 91 82 87 8831 6850 .85 1.177 .937 1.852 1.225 2.741 156 620 1.179 .96 150 4280 18590 75 90 352 367 0 2736 153 2584 .637 1946 1793 1.57 .507 -.651 -.98

Total number of rows: 21504

Table truncated, full table size 4901 Kbytes.




Supplementary data files not provided
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