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Sample GSM91469 Query DataSets for GSM91469
Status Public on Jan 11, 2006
Title N2 ref. JL1 vs. spe-9;emb-27 day 14 (44E)
Sample type RNA
 
Channel 1
Source name spe-9;emb-27 day 14 (44E)
Organism Caenorhabditis elegans
Characteristics spe-9;emb-27 day 14 (44E)
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/2000-05/6368.gif
Measurement: time(absolute) 13 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
1 456 820 121 232 335 588 null null 129 300 null null null null null null null null 67 36 null null null null .57 1.755 null null 2.21 null 80 441 1.751 .86 null null null 62 73 73 84 0 964 272 692 2.066 null null .484 null 1.047 null
2 305 845 122 218 183 627 null null 126 287 null null null null null null null null 50 38 null null null null .292 3.426 null null 3.109 null 52 313 3.094 .89 null null null 61 70 91 100 0 994 256 738 4.033 null null .248 null 2.012 null
3 282 791 119 221 163 570 null null 124 269 null null null null null null null null 48 48 null null null null .286 3.497 null null 3.261 null 52 312 2.935 .88 null null null 62 71 105 114 0 930 260 670 4.11 null null .243 null 2.039 null
4 291 886 116 210 175 676 null null 131 355 null null null null null null null null 35 25 null null null null .259 3.863 null null 2.822 null 80 426 4.299 .75 null null null 63 74 121 132 0 1042 247 795 4.543 null null .22 null 2.184 null
5 263 656 119 210 144 446 null null 133 360 null null null null null null null null 35 20 null null null null .323 3.097 null null 2.639 null 80 444 3.149 .66 null null null 60 71 139 150 0 771 247 524 3.639 null null .275 null 1.863 null
6 183 440 118 193 65 247 null null 125 271 null null null null null null null null 31 20 null null null null .263 3.8 null null 2.51 null 80 419 3.215 .44 null null null 59 70 155 166 0 517 227 290 4.462 null null .224 null 2.158 null
7 442 643 116 190 326 453 null null 123 254 null null null null null null null null 51 40 null null null null .72 1.39 null null 1.519 null 120 518 1.231 .82 null null null 59 72 169 182 0 756 223 533 1.635 null null .612 null .709 null
8 234 610 114 184 120 426 null null 120 234 null null null null null null null null 37 37 null null null null .282 3.55 null null 2.84 null 80 391 2.63 .79 null null null 60 71 187 198 0 717 216 501 4.175 null null .24 null 2.062 null
9 562 2160 119 177 443 1983 null null 124 224 null null null null null null null null 56 56 null null null null .223 4.476 null null 3.044 null 52 282 2.678 .57 null null null 61 70 204 213 0 2541 208 2333 5.266 null null .19 null 2.397 null
10 256 634 122 193 134 441 null null 126 236 null null null null null null null null 38 37 null null null null .304 3.291 null null 2.59 null 80 378 2.644 .88 null null null 60 71 218 229 0 745 227 518 3.866 null null .259 null 1.951 null
11 402 654 115 197 287 457 null null 123 231 null null null null null null null null 45 46 null null null null .628 1.592 null null 1.589 null 120 523 1.289 .85 null null null 58 71 234 247 0 769 231 538 1.875 null null .533 null .907 null
12 1612 1700 120 209 1492 1491 null null 127 251 null null null null null null null null 72 60 null null null null 1.001 .999 null null 1.072 null 120 532 .945 .95 null null null 58 71 250 263 0 2000 245 1755 1.176 null null .85 null .234 null
13 327 733 117 194 210 539 null null 124 238 null null null null null null null null 91 75 null null null null .39 2.567 null null 2.24 null 80 402 2.133 .88 null null null 59 70 268 279 0 862 228 634 3.019 null null .331 null 1.594 null
14 186 334 113 183 73 151 null null 121 227 null null null null null null null null 31 40 null null null null .483 2.068 null null 2.215 null 80 409 1.816 .69 null null null 59 70 282 293 0 392 215 177 2.425 null null .412 null 1.278 null
15 214 420 111 197 103 223 null null 120 258 null null null null null null null null 55 36 null null null null .462 2.165 null null 1.912 null 80 408 1.657 .61 null null null 60 71 298 309 0 494 231 263 2.553 null null .392 null 1.352 null
16 279 431 112 195 167 236 null null 120 251 null null null null null null null null 66 36 null null null null .708 1.413 null null 1.42 null 120 534 1.249 .47 null null null 59 72 313 326 -100 507 229 278 1.665 null null .601 null .735 null
17 295 443 116 197 179 246 null null 122 258 null null null null null null null null 50 27 null null null null .728 1.374 null null 1.791 null 80 382 1.291 .61 null null null 61 72 331 342 0 521 231 290 1.62 null null .617 null .696 null
18 253 461 117 198 136 263 null null 123 248 null null null null null null null null 47 35 null null null null .517 1.934 null null 1.929 null 80 377 1.489 .7 null null null 61 72 347 358 0 542 232 310 2.279 null null .439 null 1.189 null
19 240 471 115 189 125 282 null null 123 248 null null null null null null null null 48 26 null null null null .443 2.256 null null 2.126 null 80 313 1.78 .58 null null null 62 73 362 373 0 554 222 332 2.656 null null .377 null 1.409 null
20 427 504 114 181 313 323 null null 121 252 null null null null null null null null 52 24 null null null null .969 1.032 null null 1.329 null 120 427 .974 .64 null null null 60 73 378 391 0 592 212 380 1.214 null null .824 null .28 null

Total number of rows: 20736

Table truncated, full table size 4904 Kbytes.




Supplementary data files not provided
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