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Sample GSM75962 Query DataSets for GSM75962
Status Public on Sep 24, 2005
Title DES460(wt) vs. DES459(mec1) genomic DNA comparison #2
Sample type genomic
 
Channel 1
Source name DES459(mec1)
Organism Saccharomyces cerevisiae
Characteristics DES459(mec1)
Extracted molecule genomic DNA
Label Cy3
 
Channel 2
Source name DES460 (wt)
Organism Saccharomyces cerevisiae
Characteristics DES460 (wt)
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: Genomic DNA, DNA.ch.pt
Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/9844.gif
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 Sep 23, 2005
Last update date Sep 22, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) array@genome.stanford.edu
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 GPL2658
Series (1)
GSE3358 DNA damage responses and Mec1p

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 values 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 value of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized value 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 value of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized value 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 2244 1445 365 225 1879 1220 null null 372 233 null null null null null null null null 100 100 null null null null 1.54 .649 null null .652 null 80 461 .651 .95 null null null 26 36 28 38 0 1806 281 1525 .812 null null 1.232 null -.301 null
2 440 281 353 217 87 64 null null 354 219 null null null null null null null null 35 35 null null null null 1.359 .736 null null .689 null 80 432 .464 .68 null null null 27 37 43 53 0 351 271 80 .92 null null 1.088 null -.121 null
3 2979 2339 352 213 2627 2126 null null 356 216 null null null null null null null null 100 100 null null null null 1.236 .809 null null .792 null 80 498 .76 .98 null null null 27 37 63 73 0 2923 266 2657 1.011 null null .989 null .016 null
4 1580 1000 354 213 1226 787 null null 359 219 null null null null null null null null 100 100 null null null null 1.558 .642 null null .639 null 12 98 .595 .94 null null null 28 33 83 88 0 1250 266 984 .803 null null 1.246 null -.317 null
5 1564 1082 369 221 1195 861 null null 376 232 null null null null null null null null 100 96 null null null null 1.388 .721 null null .696 null 32 170 .701 .97 null null null 28 34 99 105 0 1352 276 1076 .9 null null 1.111 null -.151 null
6 563 331 368 226 195 105 null null 370 230 null null null null null null null null 41 40 null null null null 1.857 .538 null null .525 null 80 478 .46 .88 null null null 26 36 113 123 0 413 282 131 .672 null null 1.489 null -.574 null
7 5701 2687 362 223 5339 2464 null null 380 240 null null null null null null null null 100 100 null null null null 2.167 .462 null null .465 null 80 434 .469 .98 null null null 26 36 133 143 0 3358 278 3080 .577 null null 1.733 null -.794 null
8 374 222 354 222 20 null null null 358 222 null null null null null null null null 23 10 null null null null null null null null .49 null 80 404 -.028 -.04 null null null 26 36 148 158 0 277 277 null null null null null null null null
9 371 214 357 220 14 -6 null null 357 222 null null null null null null null null 18 11 null null null null null null null null .891 null 80 432 .07 .11 null null null 26 36 165 175 0 267 275 -8 null null null null null null null
10 349 225 355 219 -6 6 null null 359 220 null null null null null null null null 20 20 null null null null null null null null .323 null 80 434 .01 0 null null null 26 36 182 192 0 281 273 8 null null null null null null null
11 350 228 360 221 -10 7 null null 362 222 null null null null null null null null 12 18 null null null null null null null null .628 null 80 444 .047 .07 null null null 26 36 200 210 0 285 276 9 null null null null null null null
12 359 229 365 221 -6 8 null null 368 225 null null null null null null null null 8 12 null null null null null null null null .571 null 80 433 .017 .03 null null null 26 36 217 227 0 286 276 10 null null null null null null null
13 362 220 365 227 -3 -7 null null 368 232 null null null null null null null null 15 6 null null null null null null null null .711 null 80 432 .059 .08 null null null 26 36 235 245 0 275 283 -8 null null null null null null null
14 388 233 366 228 22 5 null null 367 231 null null null null null null null null 30 16 null null null null 4.4 .227 null null .688 null 80 420 .077 .13 null null null 26 36 252 262 0 291 285 6 .273 null null 3.667 null -1.874 null
15 375 235 373 236 2 -1 null null 375 239 null null null null null null null null 16 11 null null null null null null null null .45 null 80 433 .002 0 null null null 26 36 269 279 0 293 295 -2 null null null null null null null
16 383 233 375 233 8 null null null 377 235 null null null null null null null null 12 5 null null null null null null null null .47 null 80 444 .053 .09 null null null 26 36 287 297 0 291 291 null null null null null null null null
17 379 231 373 233 6 -2 null null 376 235 null null null null null null null null 26 6 null null null null null null null null .609 null 80 420 .033 .05 null null null 26 36 304 314 0 288 291 -3 null null null null null null null
18 382 234 367 233 15 1 null null 398 255 null null null null null null null null 0 0 null null null null 15 .067 null null .742 null 80 430 .068 .1 null null null 25 35 321 331 0 292 291 1 .067 null null 15 null -3.907 null
19 384 237 380 239 4 -2 null null 527 348 null null null null null null null null 2 1 null null null null null null null null .643 null 80 440 .662 .95 null null null 25 35 339 349 0 296 298 -2 null null null null null null null
20 416 245 374 232 42 13 null null 375 233 null null null null null null null null 18 20 null null null null 3.231 .31 null null .492 null 80 430 .325 .69 null null null 25 35 356 366 0 306 290 16 .381 null null 2.625 null -1.392 null

Total number of rows: 8064

Table truncated, full table size 1960 Kbytes.




Supplementary data files not provided

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