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Sample GSM91452 Query DataSets for GSM91452
Status Public on Jan 11, 2006
Title N2 ref. JL1 vs. spe-9;emb-27 day 3 (40E)
Sample type RNA
 
Channel 1
Source name spe-9;emb-27 day 3 (40E)
Organism Caenorhabditis elegans
Characteristics spe-9;emb-27 day 3 (40E)
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/2000-04/4059.gif
Measurement: time(absolute) 3 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 1088 263 103 37 985 226 null null 109 41 null null null null null null null null 83 73 null null null null 4.358 .229 null null .291 null 80 432 .192 .94 null null null 78 88 88 98 0 641 90 551 .559 null null 1.788 null -.838 null
2 437 208 101 37 336 171 null null 105 40 null null null null null null null null 61 61 null null null null 1.965 .509 null null .596 null 52 241 .455 .91 null null null 80 88 104 112 0 507 90 417 1.241 null null .806 null .312 null
3 335 216 98 33 237 183 null null 106 38 null null null null null null null null 63 82 null null null null 1.295 .772 null null .989 null 120 524 .563 .9 null null null 77 90 117 130 0 526 80 446 1.882 null null .531 null .912 null
4 736 307 98 40 638 267 null null 107 43 null null null null null null null null 79 79 null null null null 2.39 .418 null null .483 null 120 475 .373 .94 null null null 77 90 130 143 0 748 97 651 1.02 null null .98 null .029 null
5 590 283 99 42 491 241 null null 106 46 null null null null null null null null 66 70 null null null null 2.037 .491 null null .549 null 120 423 .451 .94 null null null 78 90 147 159 0 690 102 588 1.198 null null .835 null .26 null
6 373 203 95 36 278 167 null null 99 40 null null null null null null null null 71 78 null null null null 1.665 .601 null null .573 null 120 489 .506 .89 null null null 76 89 163 176 0 495 87 408 1.468 null null .681 null .553 null
7 1140 372 95 32 1045 340 null null 98 36 null null null null null null null null 67 63 null null null null 3.074 .325 null null .338 null 120 447 .311 .94 null null null 78 90 182 194 0 907 78 829 .793 null null 1.261 null -.334 null
8 553 211 95 34 458 177 null null 99 37 null null null null null null null null 76 73 null null null null 2.588 .386 null null .415 null 52 246 .33 .89 null null null 81 90 199 208 0 514 82 432 .943 null null 1.06 null -.084 null
9 467 182 93 40 374 142 null null 100 45 null null null null null null null null 63 72 null null null null 2.634 .38 null null .533 null 80 275 .265 .85 null null null 81 91 215 225 0 443 97 346 .925 null null 1.081 null -.112 null
10 662 286 104 55 558 231 null null 111 60 null null null null null null null null 76 75 null null null null 2.416 .414 null null .467 null 120 351 .361 .93 null null null 79 91 230 242 0 697 134 563 1.009 null null .991 null .013 null
11 845 312 98 40 747 272 null null 103 46 null null null null null null null null 61 57 null null null null 2.746 .364 null null .386 null 120 322 .34 .92 null null null 79 91 245 257 0 760 97 663 .888 null null 1.127 null -.172 null
12 3201 3200 102 39 3099 3161 null null 109 45 null null null null null null null null 91 96 null null null null .98 1.02 null null 1.067 null 156 563 .986 .96 null null null 77 92 258 273 0 7804 95 7709 2.488 null null .402 null 1.315 null
13 349 244 99 36 250 208 null null 107 42 null null null null null null null null 68 62 null null null null 1.202 .832 null null .72 null 80 340 .616 .71 null null null 80 90 278 288 0 595 87 508 2.032 null null .492 null 1.023 null
14 474 241 99 38 375 203 null null 105 43 null null null null null null null null 78 76 null null null null 1.847 .541 null null .561 null 80 318 .495 .91 null null null 82 92 294 304 0 587 92 495 1.32 null null .758 null .401 null
15 513 271 103 37 410 234 null null 108 42 null null null null null null null null 77 73 null null null null 1.752 .571 null null .555 null 80 390 .523 .91 null null null 80 91 309 320 0 660 90 570 1.39 null null .719 null .475 null
16 742 285 114 50 628 235 null null 122 56 null null null null null null null null 60 56 null null null null 2.672 .374 null null .447 null 120 436 .365 .93 null null null 80 92 325 337 -100 695 121 574 .914 null null 1.094 null -.13 null
17 868 346 127 73 741 273 null null 139 80 null null null null null null null null 60 53 null null null null 2.714 .368 null null .479 null 120 393 .358 .94 null null null 81 93 341 353 0 843 178 665 .897 null null 1.114 null -.156 null
18 853 313 133 84 720 229 null null 143 90 null null null null null null null null 82 68 null null null null 3.144 .318 null null .359 null 80 262 .293 .87 null null null 84 94 358 368 0 763 204 559 .776 null null 1.288 null -.365 null
19 1215 379 139 102 1076 277 null null 148 105 null null null null null null null null 72 62 null null null null 3.884 .257 null null .298 null 80 280 .235 .92 null null null 83 94 373 384 0 924 248 676 .628 null null 1.592 null -.671 null
20 2004 612 148 109 1856 503 null null 154 112 null null null null null null null null 62 54 null null null null 3.69 .271 null null .34 null 120 367 .275 .96 null null null 80 92 389 401 0 1492 265 1227 .661 null null 1.513 null -.597 null

Total number of rows: 21504

Table truncated, full table size 5125 Kbytes.




Supplementary data files not provided
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