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Sample GSM211535 Query DataSets for GSM211535
Status Public on Jul 19, 2007
Title N2 (red, channel 2) vs. lin-14 (n179ts) (green, channel 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/2000-02/2124.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 1258 1083 339 201 919 882 null null 345 216 null null null null null null null null 70 55 null null null null 1.042 .96 null null .955 null 120 739 .974 .958 null null null 113 126 1808 1821 0 1152 213 939 1.022 null null .979 null .031 null
2 417 224 326 195 91 29 null null 356 222 null null null null null null null null 80 50 null null null null 3.138 .319 null null .962 null 120 803 .285 .391 null null null 1009 1022 1801 1814 -100 238 207 31 .341 null null 2.935 null -1.554 null
3 502 309 321 194 181 115 null null 327 209 null null null null null null null null 45 35 null null null null 1.574 .635 null null .833 null 120 579 .485 .633 null null null 130 143 1806 1819 0 328 206 122 .674 null null 1.484 null -.569 null
4 386 222 319 190 67 32 null null 326 199 null null null null null null null null 21 23 null null null null 2.094 .478 null null .742 null 120 649 .399 .52 null null null 1029 1042 1801 1814 0 236 202 34 .507 null null 1.971 null -.979 null
5 469 311 333 199 136 112 null null 333 212 null null null null null null null null 28 31 null null null null 1.214 .824 null null 1.028 null 120 609 .732 .771 null null null 150 163 1805 1818 0 330 211 119 .875 null null 1.143 null -.193 null
6 539 300 329 191 210 109 null null 335 205 null null null null null null null null 46 31 null null null null 1.927 .519 null null .619 null 120 655 .517 .693 null null null 1049 1062 1801 1814 0 319 203 116 .552 null null 1.81 null -.856 null
7 632 504 328 196 304 308 null null 331 209 null null null null null null null null 55 50 null null null null .987 1.013 null null .778 null 120 578 .836 .794 null null null 172 184 1807 1819 0 536 208 328 1.079 null null .927 null .11 null
8 649 521 332 195 317 326 null null 338 205 null null null null null null null null 50 46 null null null null .972 1.028 null null 1.341 null 120 674 .907 .886 null null null 1070 1083 1801 1814 0 554 207 347 1.095 null null .914 null .13 null
9 989 1743 327 199 662 1544 null null 330 210 null null null null null null null null 70 78 null null null null .429 2.332 null null 2.42 null 120 577 1.871 .843 null null null 190 203 1805 1818 0 1854 211 1643 2.482 null null .403 null 1.311 null
10 545 321 325 196 220 125 null null 333 206 null null null null null null null null 47 38 null null null null 1.76 .568 null null .683 null 120 639 .486 .684 null null null 1090 1103 1801 1814 0 341 208 133 .605 null null 1.654 null -.726 null
11 1098 428 326 189 772 239 null null 327 198 null null null null null null null null 74 56 null null null null 3.23 .31 null null .471 null 120 594 .032 .27 null null null 210 223 1807 1820 -100 455 201 254 .329 null null 3.039 null -1.604 null
12 1247 1021 328 205 919 816 null null 333 209 null null null null null null null null 77 79 null null null null 1.126 .888 null null .888 null 120 569 .855 .938 null null null 1112 1125 1801 1814 0 1086 218 868 .945 null null 1.059 null -.082 null
13 2011 1969 332 196 1679 1773 null null 336 205 null null null null null null null null 85 90 null null null null .947 1.056 null null 1.059 null 156 901 .996 .934 null null null 560 575 1803 1818 0 2094 208 1886 1.123 null null .89 null .168 null
14 1185 396 321 192 864 204 null null 326 202 null null null null null null null null 67 56 null null null null 4.235 .236 null null .237 null 120 819 .216 .728 null null null 1460 1473 1801 1814 0 421 204 217 .251 null null 3.982 null -1.993 null
15 8394 9985 339 202 8055 9783 null null 341 211 null null null null null null null null 78 79 null null null null .823 1.215 null null 1.241 null 208 675 1.18 .957 null null null 580 596 1803 1819 0 10622 214 10408 1.292 null null .774 null .37 null
16 987 585 331 191 656 394 null null 332 202 null null null null null null null null 65 50 null null null null 1.665 .601 null null .701 null 120 578 .553 .875 null null null 1482 1495 1801 1814 0 622 203 419 .639 null null 1.566 null -.647 null
17 1589 2268 337 201 1252 2067 null null 337 209 null null null null null null null null 71 80 null null null null .606 1.651 null null 1.703 null 156 672 1.621 .964 null null null 600 615 1803 1818 0 2412 213 2199 1.756 null null .569 null .813 null
18 567 420 334 192 233 228 null null 338 203 null null null null null null null null 42 46 null null null null 1.022 .979 null null 1.092 null 156 646 .792 .877 null null null 1500 1515 1799 1814 0 446 204 242 1.039 null null .963 null .055 null
19 502 328 333 198 169 130 null null 332 205 null null null null null null null null 40 40 null null null null 1.3 .769 null null .867 null 120 561 .571 .718 null null null 623 635 1804 1816 0 348 210 138 .817 null null 1.225 null -.292 null
20 2304 2988 333 196 1971 2792 null null 339 204 null null null null null null null null 81 82 null null null null .706 1.417 null null 1.39 null 156 733 1.395 .976 null null null 1520 1535 1800 1815 0 3178 208 2970 1.507 null null .664 null .592 null

Total number of rows: 13323

Table truncated, full table size 3217 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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