NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM64907 Query DataSets for GSM64907
Status Public on Jul 21, 2005
Title N2 control #1 (red, channel 2) vs. progesterone 10e-09 (green, channel 1)
Sample type RNA
 
Channel 1
Source name progesterone 10e-09 (green)
Organism Caenorhabditis elegans
Characteristics progesterone 10e-09 (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/2000-09/10417.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
1 689 653 66 118 623 535 null null 103 145 null null null null null null null null 62 66 null null null null 1.164 .859 null null .806 null 156 711 .815 .89 null null null 87 101 79 93 0 666 120 546 .876 null null 1.141 null -.19 null
2 397 316 67 113 330 203 null null 97 129 null null null null null null null null 87 87 null null null null 1.626 .615 null null .629 null 80 352 .588 .84 null null null 87 98 96 107 0 322 115 207 .627 null null 1.594 null -.673 null
3 147 203 59 114 88 89 null null 83 125 null null null null null null null null 34 56 null null null null .989 1.011 null null 1.269 null 52 329 .393 .55 null null null 86 95 112 121 0 207 116 91 1.034 null null .967 null .048 null
4 536 416 62 117 474 299 null null 89 139 null null null null null null null null 63 64 null null null null 1.585 .631 null null .619 null 120 476 .563 .87 null null null 86 98 128 140 0 424 119 305 .643 null null 1.554 null -.636 null
5 423 772 69 132 354 640 null null 100 161 null null null null null null null null 50 55 null null null null .553 1.808 null null 1.761 null 120 442 1.141 .74 null null null 87 99 144 156 0 787 134 653 1.845 null null .542 null .883 null
6 75 135 64 126 11 9 null null 96 153 null null null null null null null null 3 7 null null null null 1.222 .818 null null 1.571 null 80 379 .885 .76 null null null 87 97 155 165 0 137 128 9 .818 null null 1.222 null -.29 null
7 1594 1354 85 134 1509 1220 null null 106 144 null null null null null null null null 90 95 null null null null 1.237 .808 null null .787 null 80 492 .779 .95 null null null 87 98 176 187 0 1381 136 1245 .825 null null 1.212 null -.277 null
8 846 964 135 166 711 798 null null 153 175 null null null null null null null null 76 86 null null null null .891 1.122 null null 1.06 null 52 243 1.032 .97 null null null 88 97 192 201 0 983 169 814 1.145 null null .873 null .195 null
9 3791 3540 149 175 3642 3365 null null 169 193 null null null null null null null null 82 79 null null null null 1.082 .924 null null .869 null 208 1005 .948 .98 null null null 84 101 205 222 0 3612 178 3434 .943 null null 1.061 null -.085 null
10 482 682 127 162 355 520 null null 145 172 null null null null null null null null 95 98 null null null null .683 1.465 null null 1.473 null 80 367 1.117 .84 null null null 86 97 224 235 0 695 165 530 1.493 null null .67 null .578 null
11 1329 1036 85 129 1244 907 null null 91 135 null null null null null null null null 88 91 null null null null 1.372 .729 null null .721 null 80 427 .695 .96 null null null 87 98 240 251 0 1057 131 926 .744 null null 1.343 null -.426 null
12 141 213 61 118 80 95 null null 72 127 null null null null null null null null 61 53 null null null null .842 1.188 null null 1.188 null 52 258 .961 .44 null null null 87 95 261 269 0 217 120 97 1.213 null null .825 null .278 null
13 962 959 54 116 908 843 null null 57 121 null null null null null null null null 93 90 null null null null 1.077 .928 null null .909 null 80 445 .942 .97 null null null 87 98 271 282 0 978 118 860 .947 null null 1.056 null -.078 null
14 141 211 54 119 87 92 null null 56 118 null null null null null null null null 93 78 null null null null .946 1.057 null null 1.08 null 32 236 .725 .58 null null null 88 95 290 297 0 215 121 94 1.08 null null .926 null .112 null
15 131 208 55 121 76 87 null null 73 224 null null null null null null null null 1 0 null null null null .874 1.145 null null 1.446 null 52 348 .895 .69 null null null 88 97 305 314 0 212 123 89 1.171 null null .854 null .228 null
16 250 317 51 115 199 202 null null 55 119 null null null null null null null null 90 85 null null null null .985 1.015 null null 1.028 null 80 443 .938 .85 null null null 87 98 320 331 0 323 117 206 1.035 null null .966 null .05 null
17 1531 1312 47 107 1484 1205 null null 51 112 null null null null null null null null 92 95 null null null null 1.232 .812 null null .786 null 80 399 .789 .96 null null null 87 98 336 347 0 1338 109 1229 .828 null null 1.207 null -.272 null
18 145 225 46 100 99 125 null null 53 109 null null null null null null null null 71 76 null null null null .792 1.263 null null 1.253 null 80 317 .842 .75 null null null 87 97 353 363 0 229 102 127 1.283 null null .78 null .359 null
19 587 632 47 104 540 528 null null 53 110 null null null null null null null null 74 78 null null null null 1.023 .978 null null 1.062 null 120 457 .951 .95 null null null 85 97 367 379 0 644 106 538 .996 null null 1.004 null -.005 null
20 1692 1227 48 106 1644 1121 null null 53 110 null null null null null null null null 82 78 null null null null 1.467 .682 null null .723 null 120 452 .661 .97 null null null 86 98 383 395 0 1252 108 1144 .696 null null 1.437 null -.523 null

Total number of rows: 21504

Table truncated, full table size 5077 Kbytes.




Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap