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Sample GSM62233 Query DataSets for GSM62233
Status Public on Jun 25, 2005
Title vhl-1 2N vs. vhl-1 2H
Sample type RNA
 
Channel 1
Source name vhl-1 2H
Organism Caenorhabditis elegans
Characteristics vhl-1 2H
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name vhl-1 2N
Organism Caenorhabditis elegans
Characteristics vhl-1 2N
Extracted molecule total RNA
Label Cy5
 
 
Description Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-03/27041.gif; format: GIF
Data processing Value is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Jun 24, 2005
Last update date Nov 23, 2005
Contact name Min Jiang
E-mail(s) [email protected]
Phone 650-725-7612
Fax 650-725-7739
Organization name Stanford University
Street address -
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL2569
Series (1)
GSE2836 Hypoxia response

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
LOG_RAT2N_MEAN 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
VALUE same as UNF_VALUE but with flagged values removed
UNF_VALUE 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 LOG_RAT2N_MEAN VALUE UNF_VALUE
1 11350 10650 87 198 11263 10452 12066 10694 91 201 11979 10496 0 0 4335 3702 29 70 100 100 100 100 21715 22475 1.078 .928 .876 1.023 .955 .399 80 414 .872 .95 100 1790 19910 90 100 110 120 0 13831 257 13574 1.205 13888 13631 .83 1.138 .269 .186 .186
2 5573 4124 89 197 5484 3927 5784 4357 102 211 5695 4160 0 0 1526 1010 117 116 100 100 100 100 9411 9855 1.396 .716 .73 .731 .721 .135 52 339 .678 .97 90 1940 19910 90 99 125 134 0 5356 256 5100 .93 5658 5403 1.075 .949 -.105 -.076 -.076
3 305 398 94 185 211 213 293 393 99 195 199 208 0 0 91 118 35 74 98 86 96 73 424 407 .991 1.009 1.045 1.285 1.013 1.242 52 284 .715 .61 80 2120 19900 90 98 144 152 0 517 240 277 1.311 510 270 .763 1.357 .391 .441 .441
4 1331 940 98 192 1233 748 1510 1074 369 510 1412 882 0 0 581 443 1577 1930 34 1 0 0 1981 2294 1.648 .607 .625 .625 .591 .342 52 271 .577 .94 80 2270 19900 90 98 159 167 0 1221 249 971 .788 1395 1145 1.269 .811 -.344 -.302 -.302
5 8645 11649 92 187 8553 11462 9864 12698 96 193 9772 12511 0 0 3216 4594 30 68 100 100 100 100 20015 22283 .746 1.34 1.28 1.577 1.348 1.133 52 302 1.293 .95 80 2430 19900 90 98 175 183 0 15129 243 14886 1.74 16491 16248 .575 1.663 .799 .734 .734
6 1155 913 90 204 1065 709 1070 898 94 210 980 694 0 0 591 236 27 70 100 100 100 100 1774 1674 1.502 .666 .708 1.129 .659 1.35 12 90 .503 .87 50 2600 19890 90 95 193 198 0 1186 265 921 .865 1166 901 1.157 .92 -.21 -.121 -.121
7 10107 4723 95 199 10012 4524 11104 5497 99 207 11009 5298 0 0 3011 1850 37 75 100 100 100 100 14536 16307 2.213 .452 .481 .451 .465 .138 32 226 .438 .95 70 2750 19900 90 97 207 214 0 6134 258 5875 .587 7139 6881 1.704 .625 -.769 -.678 -.678
8 383 549 96 221 287 328 359 536 99 215 263 315 0 0 133 193 37 83 100 91 100 83 615 578 .875 1.143 1.198 1.124 1.148 .36 12 90 1.164 .69 50 2920 19890 90 95 225 230 0 713 287 426 1.484 696 409 .674 1.555 .57 .637 .637
9 512 944 96 192 416 752 505 909 101 197 409 717 0 0 136 260 34 70 98 100 98 100 1168 1126 .553 1.808 1.753 2.536 1.723 4.412 52 368 1.579 .87 90 3080 19890 88 97 239 248 0 1226 249 977 2.348 1181 931 .426 2.277 1.231 1.187 1.187
10 798 1132 101 203 697 929 793 1108 105 208 692 905 0 0 239 355 33 75 100 100 100 100 1626 1597 .75 1.333 1.308 1.413 1.323 .58 52 305 1.209 .88 80 3240 19900 90 98 256 264 0 1470 264 1206 1.731 1439 1175 .578 1.698 .792 .764 .764
11 7059 4298 95 203 6964 4095 7630 4653 103 209 7535 4450 0 0 2331 1850 50 72 100 100 100 100 11059 11985 1.701 .588 .591 .566 .574 .21 80 493 .572 .94 110 3410 19900 88 99 271 282 0 5582 264 5318 .764 6043 5779 1.309 .767 -.389 -.383 -.383
12 377 535 96 208 281 327 382 492 102 214 286 284 0 0 98 168 40 73 100 100 100 92 608 570 .859 1.164 .993 1.289 1.111 .832 52 335 .938 .73 90 3560 19890 88 97 287 296 0 695 270 425 1.511 639 369 .662 1.29 .596 .367 .367
13 2886 2424 95 201 2791 2223 2930 2043 128 240 2835 1842 0 0 1474 1626 369 362 97 93 93 77 5014 4677 1.256 .796 .65 .788 .737 .498 80 454 .831 .94 100 3730 19900 89 99 304 314 0 3148 261 2887 1.034 2653 2392 .967 .844 .049 -.245 -.245
14 304 365 96 200 208 165 309 342 99 211 213 142 0 0 72 131 32 77 100 75 100 46 373 355 1.261 .793 .667 .924 .919 .623 32 224 .543 .5 70 3880 19900 90 97 320 327 0 474 260 214 1.03 444 184 .971 .866 .043 -.208 -.208
15 276 337 97 200 179 137 270 324 100 207 173 124 0 0 76 114 28 79 100 71 100 28 316 297 1.307 .765 .717 .968 .72 .614 32 236 .512 .43 70 4040 19900 90 97 336 343 0 438 260 178 .994 421 161 1.006 .931 -.009 -.103 -.103
16 397 495 96 198 301 297 398 447 99 207 302 249 0 0 144 206 27 75 100 88 98 71 598 551 1.013 .987 .825 1.086 .968 .767 52 288 .842 .73 80 4200 19890 89 97 352 360 0 643 257 386 1.281 581 323 .78 1.071 .358 .099 .099
17 7456 6636 96 199 7360 6437 8392 7907 99 206 8296 7708 0 0 2543 2850 29 68 100 100 100 100 13797 16004 1.143 .875 .929 .872 .884 .273 52 286 .869 .96 80 4350 19890 89 97 367 375 0 8618 258 8360 1.136 10269 10010 .88 1.207 .184 .271 .271
18 896 1032 96 200 800 832 896 1031 103 209 800 831 0 0 164 343 35 74 100 98 100 96 1632 1631 .962 1.04 1.039 1.048 1.043 .418 52 363 .912 .85 90 4520 19890 88 97 383 392 0 1340 260 1081 1.351 1339 1079 .74 1.349 .434 .432 .432
19 1805 963 93 194 1712 769 1997 919 102 199 1904 725 0 0 696 446 43 71 100 95 100 90 2481 2629 2.226 .449 .381 .442 .423 .2 80 436 .445 .9 100 4690 19890 88 98 400 410 0 1251 252 999 .583 1194 942 1.714 .495 -.778 -1.016 -1.016
20 1490 1512 93 187 1397 1325 1435 1452 100 196 1342 1265 0 0 245 311 36 70 100 100 100 100 2722 2607 1.054 .948 .943 .967 .9 .25 52 331 .873 .92 90 4840 19880 87 96 415 424 0 1964 243 1721 1.232 1886 1643 .812 1.224 .301 .292 .292

Total number of rows: 21888

Table truncated, full table size 5001 Kbytes.




Supplementary data files not provided
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