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Sample GSM70938 Query DataSets for GSM70938
Status Public on Aug 20, 2005
Title Dauer MTC#3T1 (red, channel 2) vs. RefB-JW (green, channel 1)
Sample type RNA
 
Channel 1
Source name RefB-JW (green)
Organism Caenorhabditis elegans
Characteristics RefB-JW (green)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name Dauer MTC#3T1 (red)
Organism Caenorhabditis elegans
Characteristics Dauer MTC#3T1 (red)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: dauer, development
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11166.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 Aug 18, 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 GPL2653
Series (1)
GSE3169 Global analysis of dauer gene expression in Caenorhabditis elegans

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 2379 1045 128 139 2251 906 null null 144 151 null null null null null null null null 96 77 null null null null 2.485 .402 null null 2.559 null 120 536 .397 .93 null null null 25 37 95 107 0 1971 262 1709 .759 null null 1.317 null -.397 null
2 696 633 118 140 578 493 null null 136 151 null null null null null null null null 89 87 null null null null 1.172 .853 null null 1.151 null 120 549 .785 .69 null null null 25 38 110 123 0 1194 264 930 1.609 null null .622 null .686 null
3 378 222 116 134 262 88 null null 121 137 null null null null null null null null 100 75 null null null null 2.977 .336 null null 3.066 null 32 219 .288 .57 null null null 28 35 129 136 0 418 252 166 .634 null null 1.578 null -.658 null
4 2438 1401 118 140 2320 1261 null null 121 143 null null null null null null null null 100 100 null null null null 1.84 .544 null null 1.96 null 52 306 .505 .93 null null null 29 37 144 152 0 2643 264 2379 1.025 null null .975 null .036 null
5 8942 1887 120 141 8822 1746 null null 129 143 null null null null null null null null 100 100 null null null null 5.053 .198 null null 5.191 null 52 382 .184 .97 null null null 27 36 159 168 0 3560 266 3294 .373 null null 2.678 null -1.421 null
6 4428 1124 134 144 4294 980 null null 135 140 null null null null null null null null 100 91 null null null null 4.382 .228 null null 4.197 null 12 68 .227 .95 null null null 31 35 178 182 0 2120 271 1849 .431 null null 2.322 null -1.216 null
7 1922 586 137 142 1785 444 null null 144 142 null null null null null null null null 100 98 null null null null 4.02 .249 null null 4.076 null 80 496 .246 .92 null null null 28 39 190 201 0 1105 267 838 .469 null null 2.13 null -1.091 null
8 935 468 140 141 795 327 null null 153 145 null null null null null null null null 100 100 null null null null 2.431 .411 null null 2.566 null 32 216 .384 .88 null null null 29 36 206 213 0 883 266 617 .776 null null 1.288 null -.366 null
9 9224 1927 138 138 9086 1789 null null 148 143 null null null null null null null null 100 100 null null null null 5.079 .197 null null 4.993 null 80 465 .189 .96 null null null 27 37 223 233 0 3635 260 3375 .371 null null 2.692 null -1.429 null
10 891 612 141 146 750 466 null null 152 150 null null null null null null null null 100 100 null null null null 1.609 .621 null null 1.587 null 52 282 .587 .89 null null null 30 38 239 247 0 1154 275 879 1.172 null null .853 null .229 null
11 6853 6922 138 143 6715 6779 null null 149 148 null null null null null null null null 100 100 null null null null .991 1.01 null null .966 null 120 601 1.019 .96 null null null 28 40 255 267 0 13060 269 12791 1.905 null null .525 null .93 null
12 730 377 139 149 591 228 null null 154 152 null null null null null null null null 100 100 null null null null 2.592 .386 null null 2.559 null 52 260 .334 .78 null null null 31 39 271 279 0 711 281 430 .728 null null 1.374 null -.459 null
13 3859 3559 130 146 3729 3413 null null 142 150 null null null null null null null null 100 100 null null null null 1.093 .915 null null 1.091 null 52 318 .852 .94 null null null 31 39 288 296 0 6715 275 6440 1.727 null null .579 null .788 null
14 523 341 129 140 394 201 null null 137 145 null null null null null null null null 100 93 null null null null 1.96 .51 null null 1.992 null 32 225 .363 .71 null null null 30 37 304 311 0 643 264 379 .962 null null 1.04 null -.056 null
15 1403 821 123 142 1280 679 null null 128 146 null null null null null null null null 100 100 null null null null 1.885 .53 null null 1.827 null 52 312 .444 .89 null null null 31 39 319 327 0 1549 267 1282 1.002 null null .998 null .002 null
16 772 625 118 144 654 481 null null 128 150 null null null null null null null null 100 100 null null null null 1.36 .735 null null 1.378 null 52 301 .671 .89 null null null 32 40 335 343 0 1179 271 908 1.388 null null .72 null .473 null
17 10824 11395 120 142 10704 11253 null null 128 149 null null null null null null null null 100 100 null null null null .951 1.051 null null .954 null 52 354 1.019 .98 null null null 31 40 350 359 0 21500 267 21233 1.984 null null .504 null .988 null
18 824 794 122 139 702 655 null null 131 144 null null null null null null null null 100 100 null null null null 1.072 .933 null null 1.11 null 52 299 .804 .9 null null null 32 40 367 375 0 1498 262 1236 1.761 null null .568 null .816 null
19 2256 2148 126 141 2130 2007 null null 136 143 null null null null null null null null 100 100 null null null null 1.061 .942 null null 1.061 null 52 286 .858 .94 null null null 32 40 383 391 0 4052 266 3786 1.777 null null .563 null .83 null
20 3218 720 132 138 3086 582 null null 335 253 null null null null null null null null 65 1 null null null null 5.302 .189 null null 5.286 null 120 527 .196 .94 null null null 30 42 397 409 0 1358 260 1098 .356 null null 2.811 null -1.491 null

Total number of rows: 21504

Table truncated, full table size 5189 Kbytes.




Supplementary data files not provided
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