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Sample GSM64908 Query DataSets for GSM64908
Status Public on Jul 21, 2005
Title N2 control #1 (red, channel 2) vs. progesterone 10e-07 (green, channel 1)
Sample type RNA
 
Channel 1
Source name progesterone 10e-07 (green)
Organism Caenorhabditis elegans
Characteristics progesterone 10e-07 (green)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name N2 control #1 (red)
Organism Caenorhabditis elegans
Characteristics N2 control #1 (red)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: C. elegans, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/10418.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 20, 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)
GSE2970 Caenorhabditis elegans as an environmental monitor using DNA microarray analysis.

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 3588 2062 92 416 3496 1646 null null 109 441 null null null null null null null null 95 81 null null null null 2.124 .471 null null .499 null 80 389 .462 .95 null null null 83 94 59 70 0 2193 442 1751 .501 null null 1.997 null -.998 null
2 937 1048 126 437 811 611 null null 138 458 null null null null null null null null 92 67 null null null null 1.327 .753 null null .793 null 80 395 .747 .63 null null null 81 92 73 84 0 1114 464 650 .801 null null 1.248 null -.319 null
3 295 655 102 431 193 224 null null 108 463 null null null null null null null null 76 28 null null null null .862 1.161 null null 1.419 null 52 328 .893 .46 null null null 81 90 91 100 0 696 458 238 1.233 null null .811 null .302 null
4 2494 1397 102 435 2392 962 null null 113 448 null null null null null null null null 95 80 null null null null 2.486 .402 null null .407 null 80 445 .402 .89 null null null 80 91 107 118 0 1486 462 1024 .428 null null 2.336 null -1.224 null
5 1610 3331 127 443 1483 2888 null null 136 462 null null null null null null null null 88 86 null null null null .514 1.947 null null 2.023 null 80 420 1.897 .95 null null null 80 91 122 133 0 3543 471 3072 2.071 null null .483 null 1.051 null
6 963 1253 118 429 845 824 null null 123 465 null null null null null null null null 65 62 null null null null 1.025 .975 null null 1.058 null 80 376 .886 .91 null null null 81 91 140 150 0 1332 456 876 1.037 null null .965 null .052 null
7 2807 1925 105 429 2702 1496 null null 109 448 null null null null null null null null 75 69 null null null null 1.806 .554 null null .595 null 120 434 .541 .95 null null null 80 92 155 167 0 2047 456 1591 .589 null null 1.698 null -.764 null
8 1847 1398 129 444 1718 954 null null 133 457 null null null null null null null null 86 80 null null null null 1.801 .555 null null .573 null 80 378 .506 .88 null null null 79 90 170 181 0 1487 472 1015 .591 null null 1.693 null -.759 null
9 6198 9068 152 460 6046 8608 null null 161 478 null null null null null null null null 85 79 null null null null .702 1.424 null null 1.516 null 120 399 1.389 .97 null null null 80 92 187 199 0 9646 489 9157 1.515 null null .66 null .599 null
10 517 835 168 476 349 359 null null 175 487 null null null null null null null null 60 57 null null null null .972 1.029 null null 1.306 null 120 375 .809 .7 null null null 79 91 203 215 0 888 506 382 1.095 null null .914 null .13 null
11 3433 1463 136 463 3297 1000 null null 140 474 null null null null null null null null 73 66 null null null null 3.297 .303 null null .353 null 120 408 .298 .92 null null null 79 91 219 231 0 1556 492 1064 .323 null null 3.099 null -1.632 null
12 523 681 108 437 415 244 null null 114 456 null null null null null null null null 86 56 null null null null 1.701 .588 null null .7 null 80 354 .559 .57 null null null 79 90 235 246 0 724 464 260 .627 null null 1.596 null -.675 null
13 2739 1866 88 421 2651 1445 null null 95 439 null null null null null null null null 68 65 null null null null 1.835 .545 null null .647 null 120 469 .527 .95 null null null 79 91 251 263 0 1985 447 1538 .58 null null 1.724 null -.785 null
14 487 739 79 420 408 319 null null 83 434 null null null null null null null null 86 68 null null null null 1.279 .782 null null .844 null 80 408 .657 .6 null null null 79 90 268 279 0 786 446 340 .833 null null 1.2 null -.263 null
15 585 785 75 421 510 364 null null 78 442 null null null null null null null null 88 66 null null null null 1.401 .714 null null .795 null 80 371 .622 .64 null null null 80 91 283 294 0 835 447 388 .761 null null 1.314 null -.394 null
16 750 988 75 422 675 566 null null 78 444 null null null null null null null null 79 60 null null null null 1.193 .839 null null .922 null 120 483 .824 .86 null null null 78 91 298 311 0 1051 448 603 .893 null null 1.119 null -.163 null
17 3931 2739 79 430 3852 2309 null null 83 453 null null null null null null null null 85 71 null null null null 1.668 .599 null null .643 null 120 397 .584 .97 null null null 79 91 315 327 0 2913 457 2456 .638 null null 1.568 null -.649 null
18 551 823 84 421 467 402 null null 88 454 null null null null null null null null 68 57 null null null null 1.162 .861 null null 1.047 null 120 388 .725 .78 null null null 79 91 332 344 0 875 447 428 .916 null null 1.091 null -.126 null
19 1340 1242 80 441 1260 801 null null 84 460 null null null null null null null null 77 62 null null null null 1.573 .636 null null .68 null 120 365 .616 .91 null null null 79 91 347 359 0 1321 469 852 .676 null null 1.479 null -.564 null
20 2750 2451 78 441 2672 2010 null null 81 459 null null null null null null null null 79 79 null null null null 1.329 .752 null null .812 null 120 416 .747 .96 null null null 77 90 362 375 0 2607 469 2138 .8 null null 1.25 null -.322 null

Total number of rows: 21504

Table truncated, full table size 5122 Kbytes.




Supplementary data files not provided
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