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Sample GSM211538 Query DataSets for GSM211538
Status Public on Jul 19, 2007
Title N2 (red, channel 2) vs. lin-14 (n179ts) (green, channel 1)-repeat #2
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/2000-02/2033.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 5974 3837 1800 646 4174 3191 null null 1807 653 null null null null null null null null 53 43 null null null null 1.308 .764 null null .692 null 156 987 .744 .955 null null null 42 57 1765 1780 0 4737 797 3940 .944 null null 1.059 null -.083 null
2 1405 570 1305 473 100 97 null null 1337 487 null null null null null null null null 17 25 null null null null 1.031 .97 null null .51 null 120 816 .334 .55 null null null 943 956 1766 1779 -100 703 583 120 1.2 null null .833 null .263 null
3 3401 2109 1688 417 1713 1692 null null 1704 434 null null null null null null null null 53 60 null null null null 1.012 .988 null null .791 null 120 531 .756 .827 null null null 64 77 1765 1778 0 2603 514 2089 1.219 null null .82 null .286 null
4 1552 655 1338 476 214 179 null null 1361 491 null null null null null null null null 25 35 null null null null 1.196 .836 null null .516 null 120 631 .263 .553 null null null 964 977 1767 1780 0 808 587 221 1.033 null null .968 null .046 null
5 2373 967 1612 304 761 663 null null 1618 325 null null null null null null null null 39 47 null null null null 1.148 .871 null null .741 null 120 511 .593 .82 null null null 83 96 1766 1779 0 1193 375 818 1.075 null null .93 null .104 null
6 1775 679 1260 396 515 283 null null 1281 407 null null null null null null null null 40 38 null null null null 1.82 .55 null null .575 null 120 598 .308 .631 null null null 984 997 1767 1780 0 838 488 350 .68 null null 1.471 null -.557 null
7 2524 1154 1630 272 894 882 null null 1701 402 null null null null null null null null 20 25 null null null null 1.014 .987 null null .842 null 208 804 .631 .872 null null null 100 116 1766 1782 0 1424 335 1089 1.218 null null .821 null .285 null
8 1968 926 1212 329 756 597 null null 1294 389 null null null null null null null null 23 27 null null null null 1.266 .79 null null .819 null 120 529 .561 .817 null null null 1005 1018 1767 1780 0 1143 406 737 .975 null null 1.026 null -.037 null
9 3187 1954 1664 384 1523 1570 null null 1761 489 null null null null null null null null 36 41 null null null null .97 1.031 null null .946 null 256 1024 .798 .916 null null null 120 138 1764 1782 0 2412 474 1938 1.272 null null .786 null .348 null
10 1640 648 1201 398 439 250 null null 1282 430 null null null null null null null null 90 16 null null null null 1.756 .569 null null .567 null 208 694 .086 .344 null null null 1024 1040 1768 1784 0 800 491 309 .704 null null 1.421 null -.507 null
11 2914 1335 1719 616 1195 719 null null 1792 607 null null null null null null null null 38 48 null null null null 1.662 .602 null null .691 null 120 477 .419 .803 null null null 145 158 1766 1779 -100 1648 760 888 .743 null null 1.346 null -.428 null
12 2599 1106 1217 425 1382 681 null null 1244 433 null null null null null null null null 46 52 null null null null 2.029 .493 null null .486 null 156 561 .416 .904 null null null 1043 1058 1767 1782 0 1365 524 841 .609 null null 1.643 null -.717 null
13 4648 3042 1653 733 2995 2309 null null 1686 781 null null null null null null null null 61 57 null null null null 1.297 .771 null null .782 null 156 909 .648 .831 null null null 493 508 1765 1780 0 3755 904 2851 .952 null null 1.051 null -.071 null
14 3375 1185 1298 447 2077 738 null null 1318 453 null null null null null null null null 60 50 null null null null 2.814 .355 null null .405 null 120 694 .352 .92 null null null 1397 1410 1768 1781 0 1462 551 911 .439 null null 2.28 null -1.189 null
15 7739 6258 1519 601 6220 5657 null null 1541 622 null null null null null null null null 63 65 null null null null 1.1 .909 null null .891 null 208 696 .886 .982 null null null 512 528 1765 1781 0 7725 741 6984 1.123 null null .891 null .167 null
16 3117 1096 1375 471 1742 625 null null 1395 489 null null null null null null null null 54 57 null null null null 2.787 .359 null null .387 null 120 653 .298 .862 null null null 1414 1427 1771 1784 0 1353 581 772 .443 null null 2.256 null -1.174 null
17 4700 5257 1350 330 3350 4927 null null 1380 388 null null null null null null null null 82 92 null null null null .68 1.471 null null 1.547 null 156 709 1.315 .958 null null null 533 548 1767 1782 0 6490 407 6083 1.816 null null .551 null .861 null
18 2275 1083 1425 490 850 593 null null 1440 504 null null null null null null null null 35 47 null null null null 1.433 .698 null null .614 null 120 503 .534 .881 null null null 1438 1450 1769 1781 0 1337 604 733 .862 null null 1.16 null -.214 null
19 2847 1441 1267 228 1580 1213 null null 1295 249 null null null null null null null null 53 60 null null null null 1.303 .768 null null .638 null 120 464 .645 .863 null null null 556 568 1769 1781 0 1779 281 1498 .948 null null 1.055 null -.077 null
20 6901 9103 1387 487 5514 8616 null null 1400 497 null null null null null null null null 81 92 null null null null .64 1.563 null null 1.556 null 156 728 1.46 .961 null null null 1455 1470 1769 1784 0 11238 601 10637 1.929 null null .518 null .948 null

Total number of rows: 13323

Table truncated, full table size 3274 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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