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Sample GSM211537 Query DataSets for GSM211537
Status Public on Jul 19, 2007
Title N2 (red, channel 2) vs. lin-14 (n179ts) (green, channel 1)- repeat #1
Sample type RNA
 
Channel 1
Source name lin-14 (n179ts) (green)
Organism Caenorhabditis elegans
Characteristics lin-14 (n179ts) (green)
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name N2 (red)
Organism Caenorhabditis elegans
Characteristics N2 (red)
Extracted molecule total RNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol not provided
Description Simple annotation: Development, lin-14
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2125.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 18, 2007
Last update date Jul 18, 2007
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 GPL14
Series (1)
GSE8520 LIN-14 mutants

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 4109 3433 704 258 3405 3175 null null 712 271 null null null null null null null null 73 76 null null null null 1.072 .932 null null .934 null 120 781 .892 .94 null null null 80 93 1825 1838 0 3691 277 3414 1.003 null null .997 null .004 null
2 754 327 639 264 115 63 null null 666 294 null null null null null null null null 90 10 null null null null 1.825 .548 null null .669 null 120 792 .237 .365 null null null 978 991 1823 1836 -100 351 283 68 .591 null null 1.691 null -.758 null
3 1235 559 722 254 513 305 null null 736 267 null null null null null null null null 41 35 null null null null 1.682 .595 null null .719 null 120 604 .565 .87 null null null 99 112 1823 1836 0 601 273 328 .639 null null 1.564 null -.645 null
4 868 420 642 255 226 165 null null 641 267 null null null null null null null null 28 28 null null null null 1.37 .73 null null .606 null 120 650 .552 .809 null null null 998 1011 1824 1837 0 451 274 177 .783 null null 1.277 null -.353 null
5 1087 572 683 236 404 336 null null 688 242 null null null null null null null null 31 43 null null null null 1.202 .832 null null .734 null 120 617 .613 .887 null null null 119 132 1822 1835 0 615 253 362 .896 null null 1.116 null -.158 null
6 1070 556 647 263 423 293 null null 646 267 null null null null null null null null 41 44 null null null null 1.444 .693 null null .689 null 120 631 .603 .875 null null null 1018 1031 1824 1837 0 597 282 315 .745 null null 1.343 null -.425 null
7 1370 718 677 218 693 500 null null 707 228 null null null null null null null null 28 56 null null null null 1.386 .722 null null .732 null 120 585 .429 .76 null null null 141 153 1824 1836 0 772 234 538 .776 null null 1.288 null -.365 null
8 983 558 648 258 335 300 null null 654 273 null null null null null null null null 39 45 null null null null 1.117 .896 null null .947 null 120 658 .629 .812 null null null 1038 1051 1824 1837 0 600 277 323 .964 null null 1.037 null -.053 null
9 2108 2328 687 237 1421 2091 null null 722 250 null null null null null null null null 50 84 null null null null .68 1.471 null null 1.559 null 120 583 1.315 .946 null null null 159 172 1822 1835 0 2503 254 2249 1.583 null null .632 null .662 null
10 1153 564 637 253 516 311 null null 655 270 null null null null null null null null 50 44 null null null null 1.659 .603 null null .56 null 120 653 .517 .825 null null null 1058 1071 1824 1837 0 606 272 334 .647 null null 1.545 null -.628 null
11 2531 1348 714 251 1817 1097 null null 726 264 null null null null null null null null 71 81 null null null null 1.656 .604 null null .59 null 120 590 .54 .902 null null null 178 191 1824 1837 -100 1449 269 1180 .649 null null 1.54 null -.623 null
12 4031 2831 647 250 3384 2581 null null 654 262 null null null null null null null null 95 95 null null null null 1.311 .763 null null .763 null 120 626 .752 .975 null null null 1081 1094 1825 1838 0 3044 268 2776 .82 null null 1.219 null -.286 null
13 2503 2663 679 236 1824 2427 null null 692 259 null null null null null null null null 63 62 null null null null .752 1.331 null null 1.13 null 156 901 1.318 .958 null null null 528 543 1822 1837 0 2863 253 2610 1.431 null null .699 null .517 null
14 4166 1614 679 252 3487 1362 null null 719 333 null null null null null null null null 70 55 null null null null 2.56 .391 null null .391 null 120 717 .389 .702 null null null 1432 1445 1825 1838 0 1735 270 1465 .42 null null 2.38 null -1.251 null
15 7844 12361 688 220 7156 12141 null null 690 236 null null null null null null null null 70 76 null null null null .589 1.697 null null 1.728 null 208 678 1.656 .975 null null null 548 564 1822 1838 0 13291 236 13055 1.824 null null .548 null .867 null
16 3088 1982 670 251 2418 1731 null null 680 267 null null null null null null null null 79 82 null null null null 1.397 .716 null null .724 null 120 570 .682 .952 null null null 1449 1462 1824 1837 0 2131 269 1862 .77 null null 1.299 null -.377 null
17 3886 4933 689 230 3197 4703 null null 700 247 null null null null null null null null 74 83 null null null null .68 1.471 null null 1.538 null 156 653 1.433 .971 null null null 568 583 1822 1837 0 5304 247 5057 1.582 null null .632 null .662 null
18 1117 652 655 255 462 397 null null 670 266 null null null null null null null null 50 56 null null null null 1.164 .859 null null .891 null 120 550 .713 .893 null null null 1471 1483 1825 1837 0 701 274 427 .924 null null 1.082 null -.114 null
19 1023 537 715 242 308 295 null null 726 264 null null null null null null null null 40 44 null null null null 1.044 .958 null null .821 null 120 538 .565 .733 null null null 590 602 1823 1835 0 577 260 317 1.029 null null .972 null .042 null
20 3484 4744 673 247 2811 4497 null null 676 260 null null null null null null null null 76 89 null null null null .625 1.6 null null 1.554 null 156 842 1.514 .983 null null null 1489 1504 1824 1839 0 5101 265 4836 1.72 null null .581 null .783 null

Total number of rows: 13323

Table truncated, full table size 3232 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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