NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM211536 Query DataSets for GSM211536
Status Public on Jul 19, 2007
Title N2c (red, channel 2) vs. lin-4c (green, channel 1)
Sample type RNA
 
Channel 1
Source name lin-4c (green)
Organism Caenorhabditis elegans
Characteristics lin-4c (green)
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name N2c (red)
Organism Caenorhabditis elegans
Characteristics N2c (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/2001-03/14585.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
1 995 1247 63 91 932 1156 1007 1043 65 96 944 952 0 0 738 959 20 33 93 91 90 86 2088 1896 .806 1.24 1.008 1.208 1.289 2.409 120 571 1.279 .96 120 1850 19090 51 63 67 79 0 1405 103 1303 1.398 1175 1073 .715 1.136 .483 .184
2 491 401 63 92 428 309 432 366 65 96 369 274 0 0 326 254 21 34 91 79 84 75 737 643 1.385 .722 .743 .675 .708 1.952 120 497 .735 .93 130 2020 19100 51 64 83 96 0 452 104 348 .814 412 309 1.229 .837 -.298 -.257
3 153 148 63 90 90 58 127 144 66 94 64 54 0 0 85 60 21 33 72 58 58 45 148 118 1.552 .644 .844 .659 .658 2.885 80 347 .641 .6 100 2180 19100 53 63 101 111 0 167 101 65 .726 162 61 1.377 .951 -.462 -.073
4 301 277 62 91 239 186 291 261 64 95 229 170 0 0 207 162 20 32 81 77 75 66 425 399 1.285 .778 .742 .899 .799 2.73 80 420 .766 .84 110 2340 19110 53 64 116 127 0 312 103 210 .877 294 192 1.14 .837 -.189 -.258
5 909 450 62 92 847 358 428 265 64 95 366 173 0 0 910 401 20 31 75 66 73 56 1205 539 2.366 .423 .473 .507 .446 3.067 120 530 .418 .95 120 2510 19110 53 65 133 145 0 507 104 403 .476 299 195 2.1 .533 -1.07 -.909
6 189 186 59 88 130 98 171 132 62 91 112 44 0 0 109 114 20 30 81 62 75 40 228 156 1.327 .754 .393 .654 .606 2.775 32 204 .921 .76 70 2650 19110 55 62 149 156 0 210 99 110 .849 149 50 1.177 .443 -.235 -1.176
7 473 442 60 84 413 358 539 515 62 88 479 431 0 0 250 243 20 31 93 90 90 81 771 910 1.154 .867 .9 .732 .866 2.079 120 587 .895 .93 130 2830 19120 53 66 164 177 0 498 95 403 .977 580 486 1.024 1.014 -.034 .02
8 190 177 59 86 131 91 192 177 62 87 133 91 0 0 78 68 20 27 90 81 83 66 222 224 1.44 .695 .684 .705 .7 2.331 80 379 .743 .7 110 3000 19110 53 64 182 193 0 199 97 103 .783 199 103 1.277 .771 -.353 -.375
9 186 200 61 85 125 115 192 205 64 87 131 120 0 0 92 92 20 29 83 73 70 65 240 251 1.087 .92 .916 1.015 .975 2.43 120 436 .977 .81 120 3150 19120 54 66 197 209 0 225 96 130 1.037 231 135 .965 1.032 .052 .046
10 228 175 64 88 164 87 241 173 67 91 177 85 0 0 118 80 20 31 85 70 76 56 251 262 1.885 .53 .48 .57 .569 2.64 120 410 .561 .75 120 3310 19130 55 67 213 225 0 197 99 98 .598 195 96 1.673 .541 -.742 -.886
11 591 646 64 87 527 559 622 702 66 91 558 615 0 0 297 350 20 33 97 95 96 92 1086 1173 .943 1.061 1.102 .986 1.031 1.829 120 491 1.11 .92 130 3470 19120 53 66 228 241 0 728 98 630 1.195 791 693 .837 1.242 .257 .313
12 219 182 65 87 154 95 210 180 66 91 145 93 0 0 112 86 19 34 90 67 83 55 249 238 1.621 .617 .641 .653 .646 3.139 120 444 .644 .72 120 3630 19130 55 67 245 257 0 205 98 107 .695 203 105 1.439 .723 -.525 -.468
13 337 264 66 83 271 181 222 219 67 87 156 136 0 0 265 170 19 30 77 75 72 62 452 292 1.497 .668 .872 .716 .678 3.071 80 380 .619 .85 100 3790 19130 56 66 262 272 0 297 94 204 .753 247 153 1.329 .982 -.41 -.026
14 158 140 67 84 91 56 144 122 69 89 77 38 0 0 77 64 21 32 77 52 65 38 147 115 1.625 .615 .494 .66 .693 3.366 80 387 .705 .55 100 3960 19130 56 66 279 289 0 158 95 63 .693 137 43 1.442 .556 -.528 -.847
15 166 162 65 86 101 76 154 149 68 91 89 63 0 0 81 68 21 31 80 72 70 52 177 152 1.329 .752 .708 .891 .847 2.598 80 433 .781 .6 110 4110 19140 56 67 293 304 0 183 97 86 .848 168 71 1.179 .798 -.238 -.326
16 179 190 64 89 115 101 179 177 67 92 115 88 0 0 93 91 21 30 77 77 68 63 216 203 1.139 .878 .765 .998 .825 2.629 80 407 .964 .77 100 4270 19130 56 66 310 320 0 214 100 114 .99 199 99 1.01 .862 -.015 -.214
17 1026 1021 64 88 962 933 1091 879 67 92 1027 791 0 0 717 753 21 30 93 97 88 90 1895 1818 1.031 .97 .77 1.069 .896 2.26 80 449 1.003 .92 110 4440 19140 56 67 326 337 0 1151 99 1051 1.093 991 891 .915 .868 .128 -.204
18 187 184 61 89 126 95 184 168 64 93 123 79 0 0 112 94 20 31 72 69 63 55 221 202 1.326 .754 .642 .83 .78 2.501 120 512 .802 .8 120 4610 19140 56 68 343 355 0 207 100 107 .85 189 89 1.177 .724 -.235 -.466
19 370 396 61 93 309 303 379 423 65 93 318 330 0 0 162 140 22 31 95 95 92 90 612 648 1.02 .981 1.038 1.03 1.019 1.795 80 393 .967 .89 110 4740 19140 56 67 356 367 0 446 105 341 1.105 477 372 .905 1.169 .144 .226
20 196 182 62 88 134 94 180 171 66 91 118 83 0 0 109 87 23 33 76 69 69 56 228 201 1.426 .701 .703 .725 .661 2.757 120 525 .729 .72 120 4910 19150 57 69 373 385 0 205 99 106 .79 193 94 1.265 .793 -.339 -.335

Total number of rows: 21504

Table truncated, full table size 4504 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap