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Sample GSM91464 Query DataSets for GSM91464
Status Public on Jan 11, 2006
Title N2 ref. JL1 vs. spe-9;fer-15 day 4 (51E)
Sample type RNA
 
Channel 1
Source name spe-9;fer-15 day 4 (51E)
Organism Caenorhabditis elegans
Characteristics spe-9;fer-15 day 4 (51E)
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/2000-05/5802.gif
Measurement: time(absolute) 4 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 GPL3097
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
1 747 689 592 166 155 523 null null 598 172 null null null null null null null null 46 76 null null null null .296 3.374 null null 2.432 null 80 395 1.27 .64 null null null 91 101 107 117 0 274 66 208 1.34 null null .746 null .422 null
2 711 342 600 165 111 177 null null 609 173 null null null null null null null null 33 66 null null null null .627 1.595 null null 1.156 null 80 401 .45 .55 null null null 90 101 120 131 0 136 66 70 .633 null null 1.579 null -.659 null
3 891 232 601 167 290 65 null null 603 174 null null null null null null null null 40 32 null null null null 4.462 .224 null null .392 null 80 410 .011 .1 null null null 90 101 136 147 0 92 66 26 .089 null null 11.235 null -3.49 null
4 760 589 591 186 169 403 null null 602 192 null null null null null null null null 39 74 null null null null .419 2.385 null null 2.198 null 156 632 1.145 .71 null null null 89 103 152 166 0 234 74 160 .947 null null 1.056 null -.079 null
5 874 758 594 201 280 557 null null 608 206 null null null null null null null null 46 92 null null null null .503 1.989 null null 2.049 null 80 409 1.097 .77 null null null 90 101 167 178 0 301 80 221 .79 null null 1.266 null -.34 null
6 1135 564 587 208 548 356 null null 597 215 null null null null null null null null 75 65 null null null null 1.539 .65 null null .695 null 52 354 .583 .86 null null null 92 101 185 194 0 224 83 141 .258 null null 3.876 null -1.955 null
7 856 1373 579 220 277 1153 null null 589 232 null null null null null null null null 72 82 null null null null .24 4.162 null null 4.231 null 80 447 3.034 .76 null null null 91 102 201 212 0 545 87 458 1.653 null null .605 null .725 null
8 771 351 581 229 190 122 null null 589 229 null null null null null null null null 61 51 null null null null 1.557 .642 null null .566 null 52 273 .369 .6 null null null 96 105 217 226 0 139 91 48 .255 null null 3.922 null -1.972 null
9 778 402 594 230 184 172 null null 595 236 null null null null null null null null 44 63 null null null null 1.07 .935 null null .823 null 52 229 .478 .64 null null null 96 104 235 243 0 160 91 68 .371 null null 2.694 null -1.43 null
10 941 1139 606 217 335 922 null null 603 232 null null null null null null null null 67 87 null null null null .363 2.752 null null 1.96 null 80 309 2.126 .81 null null null 93 103 251 261 0 452 86 366 1.093 null null .915 null .128 null
11 1010 788 618 203 392 585 null null 622 212 null null null null null null null null 81 80 null null null null .67 1.492 null null 1.293 null 80 283 1.35 .83 null null null 94 105 264 275 0 313 81 232 .593 null null 1.687 null -.755 null
12 1583 13444 624 207 959 13237 null null 629 216 null null null null null null null null 82 95 null null null null .072 13.803 null null 13.547 null 156 626 12.488 .92 null null null 91 106 278 293 0 5339 82 5257 5.481 null null .182 null 2.455 null
13 1376 893 619 207 757 686 null null 628 220 null null null null null null null null 68 80 null null null null 1.103 .906 null null .803 null 120 541 .469 .54 null null null 93 106 295 308 0 355 82 272 .36 null null 2.779 null -1.474 null
14 951 620 628 193 323 427 null null 631 199 null null null null null null null null 60 61 null null null null .756 1.322 null null .827 null 80 378 1.145 .84 null null null 94 104 315 325 0 246 77 170 .525 null null 1.905 null -.93 null
15 944 771 626 196 318 575 null null 627 201 null null null null null null null null 57 68 null null null null .553 1.808 null null 1.244 null 120 476 1.767 .87 null null null 94 106 329 341 0 306 78 228 .718 null null 1.393 null -.478 null
16 995 969 622 191 373 778 null null 622 198 null null null null null null null null 63 92 null null null null .479 2.086 null null 1.863 null 52 291 1.661 .83 null null null 94 103 346 355 -100 385 76 309 .828 null null 1.207 null -.272 null
17 896 1140 645 196 251 944 null null 648 203 null null null null null null null null 45 77 null null null null .266 3.761 null null 3.033 null 80 347 2.381 .84 null null null 96 106 362 372 0 453 78 375 1.494 null null .67 null .579 null
18 905 602 656 187 249 415 null null 662 196 null null null null null null null null 61 80 null null null null .6 1.667 null null 1.203 null 80 353 1.196 .72 null null null 95 106 378 389 0 239 74 165 .662 null null 1.511 null -.595 null
19 851 498 656 184 195 314 null null 663 191 null null null null null null null null 55 76 null null null null .621 1.61 null null 1.239 null 80 230 1.091 .73 null null null 98 108 394 404 0 198 73 125 .639 null null 1.564 null -.645 null
20 1079 1297 663 197 416 1100 null null 674 210 null null null null null null null null 81 82 null null null null .378 2.644 null null 2.238 null 80 317 2.139 .78 null null null 95 106 408 419 0 515 78 437 1.05 null null .952 null .07 null

Total number of rows: 21504

Table truncated, full table size 5199 Kbytes.




Supplementary data files not provided
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