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Sample GSM70931 Query DataSets for GSM70931
Status Public on Aug 20, 2005
Title L1 MTC#4T5 (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#4T5 (red)
Organism Caenorhabditis elegans
Characteristics L1 MTC#4T5 (red)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Development, L1
Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13847.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 18649 31480 99 107 18550 31373 20378 35251 104 111 20279 35144 0 0 4715 9992 39 54 100 100 100 100 49923 55423 .591 1.691 1.733 1.676 1.703 .25 80 520 1.668 .98 110 1910 19240 46 57 33 44 0 25707 87 25620 1.381 28787 28699 .724 1.415 .466 .501
2 6469 35058 96 106 6373 34952 6213 36593 102 113 6117 36487 0 0 2941 7870 41 60 100 100 100 100 41325 42604 .182 5.484 5.965 5.712 5.858 .906 80 465 4.594 .92 110 2080 19240 46 57 50 61 0 28629 87 28542 4.479 29882 29796 .223 4.871 2.163 2.284
3 402 432 94 104 308 328 399 414 103 110 305 310 0 0 75 77 96 62 100 100 92 100 636 615 .939 1.065 1.016 1.129 1.025 .394 52 344 .712 .83 90 2240 19230 46 55 67 76 0 353 85 268 .87 338 253 1.15 .83 -.202 -.269
4 8617 11360 95 109 8522 11251 8923 12191 109 119 8828 12082 0 0 2106 2531 130 142 100 100 100 100 19773 20910 .757 1.32 1.369 1.36 1.371 .286 80 426 1.263 .98 100 2410 19230 46 56 84 94 0 9277 89 9188 1.078 9955 9866 .928 1.118 .109 .16
5 21526 6824 95 105 21431 6719 22963 7340 103 113 22868 7235 0 0 5186 1843 98 130 100 100 100 100 28150 30103 3.19 .314 .316 .316 .323 .052 80 447 .308 .98 100 2570 19230 46 56 100 110 0 5573 86 5487 .256 5994 5908 3.906 .258 -1.966 -1.953
6 5874 5495 98 100 5776 5395 6301 5779 104 103 6203 5679 0 0 2201 1418 32 28 100 100 100 100 11171 11882 1.071 .934 .916 1.211 .935 .979 32 210 .862 .98 70 2750 19220 46 53 119 126 0 4487 82 4406 .763 4719 4638 1.311 .748 -.391 -.42
7 14047 8030 96 104 13951 7926 15489 9234 98 106 15393 9130 0 0 4033 2498 26 29 100 100 100 100 21877 24523 1.76 .568 .593 .579 .581 .127 80 452 .562 .99 100 2890 19230 46 56 132 142 0 6557 85 6473 .464 7541 7456 2.155 .484 -1.108 -1.046
8 3953 2972 96 104 3857 2868 3850 3067 100 105 3754 2963 0 0 2088 1124 26 28 100 100 100 100 6725 6717 1.345 .744 .789 .879 .854 .347 52 272 .639 .92 80 3060 19230 47 55 150 158 0 2427 85 2342 .607 2505 2420 1.647 .645 -.72 -.634
9 38401 3185 96 103 38305 3082 41246 3505 100 105 41150 3402 0 0 9163 901 25 28 100 100 100 100 41387 44552 12.429 .08 .083 .082 .082 .024 80 388 .079 .98 100 3210 19240 47 57 164 174 0 2601 84 2517 .066 2862 2778 15.22 .068 -3.928 -3.889
10 2879 3815 96 106 2783 3709 2892 3998 101 112 2796 3892 0 0 775 1258 26 57 100 100 100 100 6492 6688 .75 1.333 1.392 1.323 1.326 .309 80 402 1.319 .97 100 3380 19230 46 56 181 191 0 3115 87 3029 1.088 3265 3178 .919 1.137 .122 .185
11 10530 18697 96 107 10434 18590 11246 20022 101 113 11150 19915 0 0 2958 5552 28 56 100 100 100 100 29024 31065 .561 1.782 1.786 1.938 1.786 1.408 80 456 1.696 .98 110 3540 19220 44 55 196 207 0 15268 87 15181 1.455 16350 16263 .687 1.459 .541 .545
12 2795 15043 98 105 2697 14938 2932 16845 101 108 2834 16740 0 0 676 4335 27 30 100 100 100 100 17635 19574 .181 5.539 5.907 5.583 5.642 1.271 80 401 5.456 .98 100 3700 19230 46 56 213 223 0 12284 86 12199 4.523 13756 13670 .221 4.824 2.177 2.27
13 7743 18019 99 105 7644 17914 8722 18034 102 108 8623 17929 0 0 2944 7938 26 29 100 100 100 100 25558 26552 .427 2.344 2.079 2.466 2.341 .859 52 335 2.352 .98 90 3860 19220 45 54 229 238 0 14715 86 14629 1.914 14727 14641 .523 1.698 .936 .764
14 3114 3858 96 106 3018 3752 573 1023 113 116 477 917 0 0 6607 6740 152 93 95 100 82 95 6770 1394 .804 1.243 1.922 1.83 1.724 .939 80 402 .979 .93 100 4020 19240 47 57 245 255 0 3151 87 3064 1.015 835 749 .985 1.57 .022 .651
15 1338 1623 95 105 1243 1518 1353 1652 100 110 1258 1547 0 0 316 340 30 30 100 100 100 100 2761 2805 .819 1.221 1.23 1.253 1.212 .241 52 335 1.122 .96 90 4180 19220 45 54 261 270 0 1325 86 1240 .997 1349 1263 1.003 1.004 -.004 .006
16 1155 1834 95 105 1060 1729 1202 1935 97 108 1107 1830 0 0 252 503 24 30 100 100 100 100 2789 2937 .613 1.631 1.653 1.632 1.652 .368 80 437 1.579 .96 110 4340 19230 45 56 276 287 0 1498 86 1412 1.332 1580 1494 .751 1.35 .414 .433
17 14691 38142 95 105 14596 38037 15262 41678 99 127 15167 41573 0 1 3682 11518 27 278 100 100 100 100 52633 56740 .384 2.606 2.741 2.573 2.665 .472 80 432 2.589 .98 110 4500 19230 45 56 292 303 0 31147 86 31062 2.128 34035 33949 .47 2.238 1.09 1.162
18 621 1045 93 108 528 937 646 1092 97 135 553 984 0 0 134 227 28 315 100 98 100 88 1465 1537 .564 1.775 1.779 1.818 1.772 .434 52 334 1.596 .95 90 4660 19220 45 54 309 318 0 853 88 765 1.449 892 804 .69 1.453 .535 .539
19 3812 7852 88 103 3724 7749 4036 8715 91 105 3948 8612 0 0 1063 2214 21 30 100 100 100 100 11473 12560 .481 2.081 2.181 2.137 2.154 .414 80 405 1.999 .97 100 4830 19210 44 54 326 336 0 6412 84 6328 1.699 7117 7033 .588 1.781 .765 .833
20 7806 4052 87 101 7719 3951 8707 4633 91 104 8620 4532 0 0 2343 1368 20 29 100 100 100 100 11670 13152 1.954 .512 .526 .536 .526 .259 80 389 .507 .98 100 4980 19220 45 55 341 351 0 3309 82 3226 .418 3783 3701 2.392 .429 -1.258 -1.22

Total number of rows: 21504

Table truncated, full table size 4769 Kbytes.




Supplementary data files not provided
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