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Sample GSM211539 Query DataSets for GSM211539
Status Public on Jul 19, 2007
Title N2a (red, channel 2) vs. lin-4a (green, channel 1)
Sample type RNA
 
Channel 1
Source name lin-4a (green)
Organism Caenorhabditis elegans
Characteristics lin-4a (green)
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name N2a (red)
Organism Caenorhabditis elegans
Characteristics N2a (red)
Extracted molecule total RNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol not provided
Description Simple annotation: C. elegans, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14583.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 18, 2007
Last update date Jul 18, 2007
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 GPL2646
Series (1)
GSE8520 LIN-14 mutants

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
1 661 762 35 68 626 694 865 868 35 71 830 800 0 0 445 523 8 25 91 91 90 88 1320 1630 .902 1.109 .964 1.109 1.189 2.199 120 625 1.141 .95 130 2170 18790 64 77 66 79 0 801 71 729 1.165 912 841 .858 1.013 .22 .018
2 349 255 33 66 316 189 380 263 34 70 347 197 0 0 174 131 9 28 95 85 94 75 505 544 1.672 .598 .568 .545 .603 2.007 120 514 .63 .91 130 2330 18800 65 78 82 95 0 268 69 199 .628 276 207 1.591 .597 -.67 -.745
3 78 99 35 71 43 28 61 91 36 74 26 20 0 0 44 39 8 25 72 48 61 25 71 46 1.536 .651 .769 1.152 1.003 3.561 80 348 1.001 .47 100 2500 18810 68 78 101 111 0 104 75 29 .684 96 21 1.461 .808 -.547 -.307
4 237 179 36 71 201 108 245 157 37 72 209 86 0 0 150 91 10 25 83 81 78 67 309 295 1.861 .537 .411 .736 .631 2.83 80 388 .554 .85 110 2660 18820 68 79 116 127 0 188 75 113 .565 165 90 1.771 .432 -.825 -1.21
5 473 405 36 71 437 334 506 398 37 73 470 327 0 0 281 218 9 25 95 93 90 88 771 797 1.308 .764 .696 .84 .758 2.421 80 478 .757 .93 110 2830 18810 67 78 133 144 0 426 75 351 .803 418 344 1.245 .731 -.316 -.452
6 66 107 35 70 31 37 49 96 36 71 14 26 0 0 37 50 9 25 63 50 48 28 68 40 .838 1.194 1.857 1.436 1.568 4.391 52 256 2.568 .43 80 2990 18810 69 77 151 159 0 112 74 39 1.254 101 27 .797 1.951 .327 .965
7 341 282 36 68 305 214 406 295 37 70 370 227 0 0 200 155 9 24 95 86 92 77 519 597 1.425 .702 .614 .71 .742 2.323 120 501 .707 .91 130 3140 18820 67 80 163 176 0 296 71 225 .737 310 239 1.356 .645 -.44 -.633
8 76 114 37 73 39 41 68 115 38 76 31 42 0 0 39 44 12 26 67 58 54 36 80 73 .951 1.051 1.355 1.377 1.324 2.75 120 450 1.43 .55 120 3300 18810 67 79 180 192 0 120 77 43 1.105 121 44 .905 1.424 .144 .51
9 137 152 36 73 101 79 146 155 37 74 110 82 0 0 53 46 8 24 97 87 92 73 180 192 1.278 .782 .745 .778 .747 2.208 80 412 .86 .77 110 3470 18820 68 79 197 208 0 160 77 83 .822 163 86 1.217 .783 -.283 -.352
10 186 132 37 71 149 61 198 124 38 73 161 53 0 0 66 43 8 23 100 80 97 61 210 214 2.443 .409 .329 .386 .418 2.056 80 357 .404 .67 110 3630 18830 69 80 213 224 0 139 75 64 .43 130 56 2.325 .346 -1.217 -1.532
11 628 521 37 72 591 449 730 546 38 74 693 474 0 0 352 306 9 23 97 90 94 88 1040 1167 1.316 .76 .684 .749 .776 1.822 120 472 .788 .95 130 3790 18820 67 80 228 241 0 547 76 472 .798 574 498 1.253 .719 -.325 -.476
12 118 123 36 72 82 51 117 121 37 74 81 49 0 0 64 56 9 24 81 59 75 50 133 130 1.608 .622 .605 .68 .623 2.31 120 425 .773 .71 120 3950 18830 69 81 245 257 0 129 76 54 .654 127 51 1.53 .636 -.614 -.654
13 342 194 35 71 307 123 268 163 36 74 233 92 0 0 292 118 8 25 88 76 85 63 430 325 2.496 .401 .395 .489 .419 2.976 80 396 .375 .87 110 4110 18830 69 80 261 272 0 204 75 129 .421 171 97 2.375 .415 -1.248 -1.269
14 90 117 35 70 55 47 85 110 36 75 50 40 0 0 42 46 8 25 85 62 75 41 102 90 1.17 .855 .8 1.037 .923 2.907 80 389 1.246 .55 100 4270 18830 70 80 278 288 0 123 74 49 .898 116 42 1.114 .841 -.155 -.25
15 80 106 35 74 45 32 77 100 36 75 42 26 0 0 40 37 8 24 80 51 72 26 77 68 1.406 .711 .619 .835 .789 2.75 80 393 1.152 .5 100 4440 18830 70 80 295 305 0 111 78 34 .747 105 27 1.338 .65 -.42 -.62
16 115 144 36 76 79 68 110 148 36 78 74 72 0 0 58 57 9 24 83 72 78 60 147 146 1.162 .861 .973 .982 .979 2.894 80 394 1.041 .66 110 4590 18840 70 81 309 320 0 151 80 71 .904 156 76 1.106 1.022 -.145 .032
17 506 478 35 72 471 406 370 364 36 75 335 292 0 0 500 430 9 23 74 70 65 65 877 627 1.16 .862 .872 1.139 .849 2.968 120 416 .853 .95 120 4760 18840 70 82 326 338 0 502 76 427 .906 382 307 1.104 .916 -.143 -.127
18 106 138 34 72 72 66 108 130 35 74 74 58 0 0 65 66 9 23 75 65 62 54 138 132 1.091 .917 .784 1.041 1.01 2.948 120 372 1.028 .74 120 4920 18840 70 82 342 354 0 145 76 69 .963 137 61 1.038 .824 -.054 -.28
19 266 204 35 74 231 130 268 196 36 76 233 122 0 0 139 105 8 25 96 80 95 69 361 355 1.777 .563 .524 .478 .538 2.81 120 438 .603 .84 120 5060 18840 70 82 356 368 0 214 78 137 .591 206 128 1.691 .55 -.758 -.862
20 130 137 35 71 95 66 134 131 36 75 99 60 0 0 71 60 8 25 83 65 78 55 161 159 1.439 .695 .606 .692 .674 2.46 120 469 .762 .73 120 5240 18840 70 82 374 386 0 144 75 69 .73 138 63 1.37 .637 -.454 -.651

Total number of rows: 21504

Table truncated, full table size 4447 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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