NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM91455 Query DataSets for GSM91455
Status Public on Jan 11, 2006
Title N2 ref. JL1 vs. spe-9;fer-15 day 6 (31E)
Sample type RNA
 
Channel 1
Source name spe-9;fer-15 day 6 (31E)
Organism Caenorhabditis elegans
Characteristics spe-9;fer-15 day 6 (31E)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name N2 ref. JL1
Organism Caenorhabditis elegans
Characteristics N2 ref. JL1
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: aging, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2000-03/3723.gif
Measurement: time(absolute) 6.5 d
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 Jan 10, 2006
Last update date Sep 22, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) [email protected]
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 GPL3096
Series (1)
GSE4005 Aging time course

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 LOG_RAT2N_MEDIANs 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 LOG_RAT2N_MEDIAN of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized LOG_RAT2N_MEDIAN of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized LOG_RAT2N_MEDIAN 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 LOG_RAT2N_MEDIAN of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized LOG_RAT2N_MEDIAN 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
1 445 238 72 42 373 196 null null 75 48 null null null null null null null null 76 61 null null null null 1.903 .525 null null .545 null 52 297 .445 .802 null null null 90 98 63 71 0 396 70 326 .874 null null 1.144 null -.194 null
2 238 132 69 46 169 86 null null 75 50 null null null null null null null null 78 65 null null null null 1.965 .509 null null .901 null 32 236 .271 .512 null null null 89 96 82 89 0 220 76 144 .852 null null 1.174 null -.231 null
3 168 97 68 44 100 53 null null 73 47 null null null null null null null null 68 59 null null null null 1.887 .53 null null .624 null 32 201 .32 .507 null null null 90 97 97 104 0 161 73 88 .88 null null 1.136 null -.184 null
4 381 105 69 44 312 61 null null 73 48 null null null null null null null null 71 53 null null null null 5.115 .196 null null .239 null 52 260 .123 .619 null null null 90 98 112 120 0 175 73 102 .327 null null 3.059 null -1.613 null
5 156 106 72 44 84 62 null null 78 48 null null null null null null null null 63 59 null null null null 1.355 .738 null null .759 null 52 317 .378 .483 null null null 90 98 128 136 0 176 73 103 1.226 null null .816 null .294 null
6 156 101 73 46 83 55 null null 78 52 null null null null null null null null 59 65 null null null null 1.509 .663 null null .675 null 52 309 .335 .512 null null null 89 97 146 154 0 168 76 92 1.108 null null .902 null .149 null
7 383 213 76 53 307 160 null null 79 57 null null null null null null null null 71 68 null null null null 1.919 .521 null null .604 null 80 409 .349 .684 null null null 90 100 160 170 0 355 88 267 .87 null null 1.15 null -.201 null
8 320 193 75 52 245 141 null null 77 56 null null null null null null null null 84 81 null null null null 1.738 .576 null null .806 null 32 225 .414 .721 null null null 90 97 177 184 0 321 86 235 .959 null null 1.043 null -.06 null
9 180 145 75 52 105 93 null null 79 55 null null null null null null null null 71 71 null null null null 1.129 .886 null null .802 null 32 227 .553 .606 null null null 91 98 193 200 0 241 86 155 1.476 null null .677 null .562 null
10 292 134 74 53 218 81 null null 76 55 null null null null null null null null 68 59 null null null null 2.691 .372 null null .593 null 32 229 .25 .574 null null null 91 98 207 214 0 223 88 135 .619 null null 1.615 null -.691 null
11 309 151 81 57 228 94 null null 85 61 null null null null null null null null 60 68 null null null null 2.426 .412 null null .43 null 80 469 .254 .615 null null null 89 99 224 234 0 251 95 156 .684 null null 1.462 null -.547 null
12 1267 1108 87 74 1180 1034 null null 92 80 null null null null null null null null 78 81 null null null null 1.141 .876 null null .879 null 80 455 .736 .821 null null null 88 99 239 250 0 1846 123 1723 1.46 null null .685 null .546 null
13 241 105 91 79 150 26 null null 93 85 null null null null null null null null 69 32 null null null null 5.769 .173 null null .587 null 52 310 .092 .249 null null null 90 98 258 266 0 175 131 44 .293 null null 3.409 null -1.769 null
14 172 98 91 73 81 25 null null 95 78 null null null null null null null null 48 42 null null null null 3.24 .309 null null .48 null 52 284 .159 .326 null null null 92 100 274 282 0 163 121 42 .519 null null 1.929 null -.948 null
15 202 132 83 77 119 55 null null 87 81 null null null null null null null null 67 51 null null null null 2.164 .462 null null .727 null 52 341 .179 .298 null null null 90 99 287 296 0 220 128 92 .773 null null 1.293 null -.371 null
16 206 147 81 82 125 65 null null 85 86 null null null null null null null null 62 56 null null null null 1.923 .52 null null .522 null 80 504 .327 .517 null null null 89 100 302 313 -100 245 136 109 .872 null null 1.147 null -.198 null
17 450 166 78 91 372 75 null null 84 94 null null null null null null null null 81 56 null null null null 4.96 .202 null null .332 null 32 231 .179 .64 null null null 90 97 321 328 0 276 151 125 .336 null null 2.976 null -1.573 null
18 196 176 81 94 115 82 null null 87 97 null null null null null null null null 63 56 null null null null 1.402 .713 null null .964 null 52 298 .41 .522 null null null 91 99 336 344 0 293 156 137 1.191 null null .839 null .253 null
19 259 335 88 94 171 241 null null 92 96 null null null null null null null null 71 68 null null null null .71 1.409 null null 1.634 null 32 236 .882 .621 null null null 91 98 353 360 0 558 156 402 2.351 null null .425 null 1.233 null
20 1099 314 87 88 1012 226 null null 91 92 null null null null null null null null 76 69 null null null null 4.478 .223 null null .282 null 52 365 .165 .787 null null null 91 100 368 377 0 523 146 377 .373 null null 2.684 null -1.425 null

Total number of rows: 20736

Table truncated, full table size 4907 Kbytes.




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