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Sample GSM91470 Query DataSets for GSM91470
Status Public on Jan 11, 2006
Title N2 ref. JL1 vs. spe-9;fer-15 day 11 (33E)
Sample type RNA
 
Channel 1
Source name spe-9;fer-15 day 11 (33E)
Organism Caenorhabditis elegans
Characteristics spe-9;fer-15 day 11 (33E)
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/2000-03/3981.gif
Measurement: time(absolute) 10 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
1 851 946 223 178 628 768 null null 226 182 null null null null null null null null 59 56 null null null null .818 1.223 null null 1.107 null 52 328 1.09 .83 null null null 63 72 64 73 0 946 178 768 1.223 null null .818 null .29 null
2 595 757 224 164 371 593 null null 226 176 null null null null null null null null 46 50 null null null null .626 1.598 null null 1.419 null 52 305 1.353 .85 null null null 64 73 80 89 0 757 164 593 1.598 null null .626 null .677 null
3 657 486 216 165 441 321 null null 218 173 null null null null null null null null 50 56 null null null null 1.374 .728 null null .812 null 52 277 .625 .92 null null null 64 72 97 105 0 486 165 321 .728 null null 1.374 null -.458 null
4 1188 640 217 176 971 464 null null 219 184 null null null null null null null null 75 56 null null null null 2.093 .478 null null .635 null 80 394 .443 .96 null null null 62 72 114 124 0 640 176 464 .478 null null 2.093 null -1.065 null
5 1026 841 235 184 791 657 null null 236 196 null null null null null null null null 69 73 null null null null 1.204 .831 null null .791 null 52 302 .678 .87 null null null 62 71 126 135 0 841 184 657 .831 null null 1.204 null -.268 null
6 810 519 242 182 568 337 null null 243 198 null null null null null null null null 70 65 null null null null 1.685 .593 null null .643 null 80 432 .478 .88 null null null 61 71 146 156 0 519 182 337 .593 null null 1.685 null -.753 null
7 1253 1105 239 188 1014 917 null null 240 203 null null null null null null null null 85 75 null null null null 1.106 .904 null null 1.047 null 80 377 .811 .94 null null null 62 72 162 172 0 1105 188 917 .904 null null 1.106 null -.145 null
8 707 556 234 192 473 364 null null 233 202 null null null null null null null null 51 48 null null null null 1.299 .77 null null 1.663 null 52 246 .676 .94 null null null 66 75 176 185 0 556 192 364 .77 null null 1.299 null -.378 null
9 490 401 235 210 255 191 null null 239 218 null null null null null null null null 36 27 null null null null 1.335 .749 null null 1.69 null 80 413 .604 .91 null null null 61 72 190 201 0 401 210 191 .749 null null 1.335 null -.417 null
10 1478 779 272 228 1206 551 null null 277 240 null null null null null null null null 81 45 null null null null 2.189 .457 null null .458 null 80 393 .466 .94 null null null 63 73 207 217 0 779 228 551 .457 null null 2.189 null -1.13 null
11 1365 750 247 208 1118 542 null null 254 217 null null null null null null null null 72 61 null null null null 2.063 .485 null null .536 null 80 412 .474 .95 null null null 63 74 224 235 0 750 208 542 .485 null null 2.063 null -1.045 null
12 2195 5504 229 199 1966 5305 null null 238 212 null null null null null null null null 81 85 null null null null .371 2.698 null null 2.648 null 120 543 2.633 .97 null null null 62 75 238 251 0 5504 199 5305 2.698 null null .371 null 1.432 null
13 411 385 259 204 152 181 null null 269 218 null null null null null null null null 44 42 null null null null .84 1.191 null null .609 null 52 329 .668 .78 null null null 64 73 256 265 0 385 204 181 1.191 null null .84 null .252 null
14 623 463 269 232 354 231 null null 270 238 null null null null null null null null 60 51 null null null null 1.532 .653 null null .845 null 80 367 .55 .83 null null null 66 76 273 283 0 463 232 231 .653 null null 1.532 null -.616 null
15 860 717 253 246 607 471 null null 255 254 null null null null null null null null 76 56 null null null null 1.289 .776 null null .832 null 52 300 .791 .93 null null null 66 75 288 297 0 717 246 471 .776 null null 1.289 null -.366 null
16 1299 767 247 256 1052 511 null null 250 265 null null null null null null null null 85 63 null null null null 2.059 .486 null null .541 null 80 459 .43 .91 null null null 63 74 304 315 -100 767 256 511 .486 null null 2.059 null -1.042 null
17 1713 1101 269 281 1444 820 null null 275 294 null null null null null null null null 70 56 null null null null 1.761 .568 null null .667 null 80 372 .555 .96 null null null 66 76 321 331 0 1101 281 820 .568 null null 1.761 null -.816 null
18 1853 1399 356 339 1497 1060 null null 383 360 null null null null null null null null 61 63 null null null null 1.412 .708 null null .895 null 52 319 .68 .95 null null null 66 75 337 346 0 1399 339 1060 .708 null null 1.412 null -.498 null
19 1738 1426 395 366 1343 1060 null null 404 378 null null null null null null null null 50 51 null null null null 1.267 .789 null null .851 null 52 255 .748 .96 null null null 68 76 355 363 0 1426 366 1060 .789 null null 1.267 null -.341 null
20 4294 1676 372 370 3922 1306 null null 378 375 null null null null null null null null 77 60 null null null null 3.003 .333 null null .365 null 80 335 .344 .96 null null null 65 75 368 378 0 1676 370 1306 .333 null null 3.003 null -1.586 null

Total number of rows: 21504

Table truncated, full table size 5210 Kbytes.




Supplementary data files not provided
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