NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM211534 Query DataSets for GSM211534
Status Public on Jul 19, 2007
Title N2b (red, channel 2) vs. lin-4b (green, channel 1)
Sample type RNA
 
Channel 1
Source name lin-4b (green)
Organism Caenorhabditis elegans
Characteristics lin-4b (green)
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name N2b (red)
Organism Caenorhabditis elegans
Characteristics N2b (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/2001-03/14584.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
1 907 707 42 115 865 592 1141 749 43 119 1099 634 0 0 549 444 10 43 90 89 88 83 1457 1733 1.461 .684 .577 .69 .666 2.298 120 625 .718 .94 130 2020 18260 11 24 95 108 0 943 153 789 .912 999 845 1.096 .769 -.132 -.379
2 461 319 42 118 419 201 473 314 43 122 431 196 0 0 222 149 10 45 98 81 95 70 620 627 2.085 .48 .455 .447 .496 2.397 120 555 .498 .81 130 2180 18260 11 24 111 124 0 425 157 268 .64 419 261 1.564 .606 -.645 -.722
3 122 186 41 118 81 68 103 170 42 123 62 52 0 0 75 74 10 46 76 52 71 35 149 114 1.191 .84 .839 1.195 .981 3.59 80 444 1.421 .53 110 2360 18270 13 24 130 141 0 248 157 91 1.119 227 69 .893 1.118 .163 .161
4 338 244 41 126 297 118 371 229 42 127 330 103 0 0 195 97 10 45 93 76 91 58 415 433 2.517 .397 .312 .488 .433 2.824 80 427 .416 .75 110 2520 18280 14 25 146 157 0 325 168 157 .53 305 137 1.888 .416 -.917 -1.265
5 948 493 41 118 907 375 1065 540 42 120 1024 422 0 0 596 260 10 43 100 87 98 82 1282 1446 2.419 .413 .412 .504 .431 2.141 80 418 .401 .91 110 2680 18290 15 26 162 173 0 657 157 500 .551 720 563 1.814 .549 -.859 -.864
6 62 141 43 110 19 31 50 129 44 114 7 19 0 0 38 60 10 45 41 36 25 15 50 26 .613 1.632 2.714 3.029 2.825 4.051 80 359 6.692 .26 100 2840 18280 15 25 179 189 0 188 147 41 2.175 172 25 .46 3.619 1.121 1.856
7 466 335 43 111 423 224 551 327 45 116 508 216 0 0 254 170 11 43 90 83 87 74 647 724 1.888 .53 .425 .591 .496 3.044 120 478 .55 .85 120 3000 18280 14 26 194 206 0 447 148 299 .706 436 288 1.416 .567 -.502 -.819
8 132 182 44 115 88 67 124 169 46 119 80 54 0 0 60 56 10 43 91 65 88 35 155 134 1.313 .761 .675 .758 .758 2.546 80 405 1.189 .52 110 3160 18290 15 26 210 221 0 243 153 89 1.015 225 72 .985 .9 .022 -.152
9 174 187 45 116 129 71 181 175 46 121 136 59 0 0 98 76 10 45 87 60 79 35 200 195 1.817 .55 .434 .704 .625 3.348 120 463 .7 .6 120 3340 18300 16 28 228 240 0 249 155 95 .734 233 79 1.363 .578 -.447 -.79
10 206 186 45 113 161 73 217 181 46 118 172 68 0 0 122 81 10 44 85 59 82 36 234 240 2.205 .453 .395 .615 .505 3.255 120 381 .512 .62 120 3490 18310 17 29 243 255 0 248 151 97 .605 241 91 1.654 .527 -.726 -.924
11 637 329 45 113 592 216 653 303 45 117 608 190 0 0 450 201 10 43 87 71 84 60 808 798 2.741 .365 .313 .399 .386 3.007 156 560 .383 .9 140 3650 18290 14 28 258 272 0 439 151 288 .486 404 253 2.056 .417 -1.04 -1.263
12 202 199 44 108 158 91 205 192 45 113 161 84 0 0 107 83 11 43 90 70 88 49 249 245 1.736 .576 .522 .591 .598 3.06 120 419 .629 .64 120 3810 18310 17 29 275 287 0 265 144 121 .768 256 112 1.302 .696 -.381 -.524
13 435 236 42 111 393 125 320 194 44 116 278 83 0 0 357 122 10 41 95 66 91 50 518 361 3.144 .318 .299 .397 .383 2.998 80 368 .293 .79 100 3970 18320 19 29 292 302 0 315 148 167 .424 259 111 2.358 .398 -1.238 -1.329
14 154 195 42 107 112 88 153 192 43 112 111 85 0 0 71 62 9 40 90 76 88 53 200 196 1.273 .786 .766 .854 .799 2.618 52 337 1.015 .6 90 4130 18300 17 26 308 317 0 260 143 117 1.048 256 113 .955 1.021 .067 .03
15 128 178 43 110 85 68 101 169 44 116 58 59 0 0 81 84 10 43 76 55 67 41 153 117 1.25 .8 1.017 1.153 1.05 3.564 80 395 1.21 .58 100 4300 18310 18 28 325 335 0 237 147 91 1.067 225 79 .938 1.356 .093 .44
16 223 217 42 114 181 103 238 198 43 119 196 84 0 0 112 96 10 42 96 78 92 50 284 280 1.757 .569 .429 .742 .729 2.332 52 321 .664 .67 90 4440 18310 18 27 339 348 0 289 152 137 .759 264 112 1.318 .571 -.398 -.807
17 1118 638 42 115 1076 523 1128 670 43 120 1086 555 0 0 778 409 9 45 96 81 90 76 1599 1641 2.057 .486 .511 .552 .526 2.385 80 452 .478 .93 110 4610 18320 18 29 355 366 0 851 153 697 .648 893 740 1.543 .681 -.626 -.554
18 235 251 42 115 193 136 254 255 43 121 212 140 0 0 88 108 10 45 97 75 96 62 329 352 1.419 .705 .66 .663 .787 2.221 80 391 .899 .68 110 4780 18320 18 29 372 383 0 335 153 181 .939 340 187 1.064 .88 -.09 -.184
19 391 263 42 114 349 149 419 254 43 119 377 140 0 0 206 114 10 45 99 80 96 66 498 517 2.342 .427 .371 .484 .453 2.492 120 447 .422 .77 120 4930 18330 19 31 387 399 0 351 152 199 .569 339 187 1.757 .495 -.813 -1.014
20 266 212 41 116 225 96 288 208 43 117 247 92 0 0 90 74 10 42 100 75 100 51 321 339 2.344 .427 .372 .423 .411 2.247 80 395 .476 .61 110 5090 18330 19 30 403 414 0 283 155 128 .569 277 123 1.758 .497 -.814 -1.01

Total number of rows: 21504

Table truncated, full table size 4584 Kbytes.




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