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Sample GSM64911 Query DataSets for GSM64911
Status Public on Jul 21, 2005
Title N2 control #2 (red, channel 2) vs. progesterone 10e-05 (green, channel 1)
Sample type RNA
 
Channel 1
Source name progesterone 10e-05 (green)
Organism Caenorhabditis elegans
Characteristics progesterone 10e-05 (green)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name N2 control #2 (red)
Organism Caenorhabditis elegans
Characteristics N2 control #2 (red)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: C. elegans, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/10423.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 Jul 20, 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 GPL2652
Series (1)
GSE2970 Caenorhabditis elegans as an environmental monitor using DNA microarray analysis.

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 1278 433 120 202 1158 231 null null 124 207 null null null null null null null null 96 61 null null null null 5.013 .199 null null .241 null 52 360 .155 .77 null null null 101 110 77 86 0 1237 577 660 .57 null null 1.755 null -.811 null
2 291 252 121 197 170 55 null null 126 200 null null null null null null null null 56 40 null null null null 3.091 .324 null null .635 null 52 324 .215 .34 null null null 100 109 93 102 0 720 562 158 .929 null null 1.076 null -.106 null
3 152 211 118 202 34 9 null null 123 205 null null null null null null null null 33 15 null null null null 3.778 .265 null null 1.368 null 80 421 -.019 0 null null null 101 111 109 119 0 602 577 25 .735 null null 1.36 null -.444 null
4 3634 2108 119 197 3515 1911 null null 123 200 null null null null null null null null 80 56 null null null null 1.839 .544 null null .943 null 52 262 .276 .63 null null null 101 109 127 135 0 6022 562 5460 1.553 null null .644 null .635 null
5 727 315 120 189 607 126 null null 123 195 null null null null null null null null 86 55 null null null null 4.817 .208 null null .333 null 52 261 .134 .63 null null null 101 109 140 148 0 900 540 360 .593 null null 1.686 null -.754 null
6 167 190 116 190 51 null null null 121 195 null null null null null null null null 41 17 null null null null null null null null .938 null 80 435 .047 .04 null null null 100 110 157 167 0 542 542 null null null null null null null null
7 534 308 112 189 422 119 null null 116 193 null null null null null null null null 81 56 null null null null 3.546 .282 null null .379 null 80 394 .257 .68 null null null 99 109 172 182 0 880 540 340 .806 null null 1.241 null -.312 null
8 153 205 107 179 46 26 null null 112 188 null null null null null null null null 48 26 null null null null 1.769 .565 null null 1.171 null 80 382 .082 .06 null null null 99 109 189 199 0 585 511 74 1.609 null null .622 null .686 null
9 160 199 109 178 51 21 null null 114 184 null null null null null null null null 37 20 null null null null 2.429 .412 null null 1.154 null 80 380 .149 .13 null null null 99 109 205 215 0 568 508 60 1.176 null null .85 null .234 null
10 152 212 110 188 42 24 null null 114 190 null null null null null null null null 35 27 null null null null 1.75 .571 null null 1.792 null 80 410 .178 .15 null null null 98 108 221 231 0 605 537 68 1.619 null null .618 null .695 null
11 335 234 114 186 221 48 null null 115 187 null null null null null null null null 84 25 null null null null 4.604 .217 null null .368 null 32 213 .284 .49 null null null 98 105 238 245 0 668 531 137 .62 null null 1.613 null -.69 null
12 1260 722 108 183 1152 539 null null 113 188 null null null null null null null null 78 73 null null null null 2.137 .468 null null .581 null 80 422 .444 .95 null null null 98 108 253 263 0 2062 522 1540 1.337 null null .748 null .419 null
13 499 324 114 185 385 139 null null 118 190 null null null null null null null null 70 53 null null null null 2.77 .361 null null .467 null 80 442 .314 .75 null null null 95 105 270 280 0 925 528 397 1.031 null null .97 null .044 null
14 271 206 121 183 150 23 null null 140 195 null null null null null null null null 56 28 null null null null 6.522 .153 null null .414 null 32 228 .107 .16 null null null 98 105 288 295 0 588 522 66 .44 null null 2.273 null -1.184 null
15 257 198 119 187 138 11 null null 122 195 null null null null null null null null 87 31 null null null null 12.545 .08 null null .501 null 32 208 .159 .17 null null null 97 104 302 309 0 565 534 31 .225 null null 4.452 null -2.154 null
16 153 191 119 193 34 -2 null null 154 200 null null null null null null null null 0 13 null null null null null null null null 1.5 null 80 426 .038 .03 null null null 96 106 316 326 0 545 551 -6 null null null null null null null
17 1494 391 118 190 1376 201 null null 150 193 null null null null null null null null 56 62 null null null null 6.846 .146 null null .163 null 80 378 .13 .83 null null null 95 105 333 343 0 1117 542 575 .418 null null 2.393 null -1.259 null
18 144 189 111 186 33 3 null null 114 187 null null null null null null null null 33 16 null null null null 11 .091 null null 1.675 null 80 396 .143 .11 null null null 95 105 348 358 0 540 531 9 .273 null null 3.667 null -1.874 null
19 450 270 108 186 342 84 null null 112 190 null null null null null null null null 84 43 null null null null 4.071 .246 null null .308 null 32 221 .192 .5 null null null 97 104 366 373 0 771 531 240 .702 null null 1.425 null -.511 null
20 616 384 108 172 508 212 null null 112 181 null null null null null null null null 61 50 null null null null 2.396 .417 null null .6 null 80 435 .345 .84 null null null 94 104 381 391 0 1097 491 606 1.193 null null .838 null .254 null

Total number of rows: 20736

Table truncated, full table size 4915 Kbytes.




Supplementary data files not provided
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