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Sample GSM62239 Query DataSets for GSM62239
Status Public on Jun 25, 2005
Title hif-1 3N vs. hif-1 3H
Sample type RNA
 
Channel 1
Source name hif-1 3H
Organism Caenorhabditis elegans
Characteristics hif-1 3H
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name hif-1 3N
Organism Caenorhabditis elegans
Characteristics hif-1 3N
Extracted molecule total RNA
Label Cy5
 
 
Description Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-03/27038.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 17675 14315 58 84 17617 14231 18585 14913 62 88 18527 14829 0 0 6104 4889 20 29 100 100 100 100 31848 33356 1.238 .808 .8 .841 .816 .239 80 426 .785 .98 100 1820 19920 71 81 93 103 0 12781 75 12706 .721 13315 13240 1.386 .715 -.471 -.485 -.485
2 9363 7112 63 95 9300 7017 10303 7870 73 102 10240 7775 0 0 2717 1995 65 56 100 100 100 100 16317 18015 1.325 .755 .759 .775 .782 .156 52 343 .716 .97 90 1970 19920 71 80 108 117 0 6350 85 6265 .674 7027 6942 1.484 .678 -.57 -.561 -.561
3 280 219 63 91 217 128 280 203 67 94 217 112 0 0 70 63 21 32 100 93 100 87 345 329 1.695 .59 .516 .642 .539 .38 32 220 .49 .71 70 2140 19910 71 78 126 133 0 196 81 114 .527 181 100 1.899 .461 -.925 -1.118 -1.118
4 2170 2016 61 94 2109 1922 2302 2352 65 95 2241 2258 0 0 761 777 18 29 100 100 100 100 4031 4499 1.097 .911 1.008 .925 .947 .288 52 280 .888 .96 80 2300 19910 71 79 142 150 0 1800 84 1716 .814 2100 2016 1.229 .9 -.297 -.153 -.153
5 13163 18052 62 95 13101 17957 13918 20249 67 97 13856 20154 0 0 3310 5166 26 30 100 100 100 100 31058 34010 .73 1.371 1.455 1.415 1.422 .399 52 361 1.35 .97 90 2460 19910 70 79 157 166 0 16118 85 16033 1.224 18079 17995 .817 1.299 .291 .377 .377
6 1070 806 62 89 1008 717 1061 715 64 94 999 626 0 0 674 461 19 30 100 100 100 100 1725 1625 1.406 .711 .627 .842 .754 .357 32 215 .677 .97 70 2630 19910 71 78 175 182 0 720 79 640 .635 638 559 1.575 .559 -.655 -.838 -.838
7 11824 6017 62 99 11762 5918 14032 6756 66 106 13970 6657 0 0 6823 3493 22 54 100 100 100 100 17680 20627 1.987 .503 .477 .546 .517 .22 52 370 .491 .98 90 2780 19920 71 80 189 198 0 5372 88 5284 .449 6032 5944 2.226 .425 -1.154 -1.233 -1.233
8 284 296 66 104 218 192 270 285 69 107 204 181 0 0 105 111 24 31 96 96 96 87 410 385 1.135 .881 .887 .938 .919 .414 32 160 .775 .84 60 2950 19910 72 78 208 214 0 264 93 171 .786 254 162 1.272 .792 -.347 -.336 -.336
9 688 2554 66 109 622 2445 674 2522 70 112 608 2413 0 0 154 413 21 34 100 100 100 100 3067 3021 .254 3.931 3.969 4.12 4.09 1.036 52 361 3.618 .94 90 3110 19910 70 79 222 231 0 2280 97 2183 3.51 2252 2154 .285 3.544 1.811 1.825 1.825
10 858 1550 67 107 791 1443 868 1597 137 148 801 1490 0 0 240 502 563 278 84 100 5 92 2234 2291 .548 1.824 1.86 1.844 1.757 .546 52 363 1.734 .95 90 3280 19920 71 80 239 248 0 1384 96 1288 1.629 1426 1330 .614 1.661 .704 .732 .732
11 9567 7047 68 113 9499 6934 9453 7126 283 206 9385 7013 0 0 1506 760 1038 444 100 100 100 100 16433 16398 1.37 .73 .747 .739 .743 .079 52 341 .649 .95 90 3440 19910 70 79 255 264 0 6292 101 6191 .652 6363 6262 1.534 .667 -.618 -.584 -.584
12 1001 1334 64 109 937 1225 982 1332 68 111 918 1223 0 0 196 222 27 33 100 100 100 100 2162 2141 .765 1.307 1.332 1.35 1.323 .317 52 340 1.181 .94 90 3590 19910 70 79 270 279 0 1191 97 1094 1.167 1189 1092 .857 1.19 .223 .25 .25
13 10357 6210 68 113 10289 6097 10433 6704 78 117 10365 6591 0 0 3220 1880 52 39 100 100 100 100 16386 16956 1.688 .593 .636 .601 .61 .124 52 362 .563 .97 90 3750 19910 70 79 286 295 0 5545 101 5444 .529 5986 5885 1.89 .568 -.918 -.817 -.817
14 270 252 68 114 202 138 272 256 74 116 204 142 0 0 62 54 29 35 100 100 100 87 340 346 1.464 .683 .696 .74 .727 .327 32 220 .582 .76 70 3910 19910 71 78 303 310 0 225 102 123 .61 229 127 1.639 .621 -.713 -.686 -.686
15 307 319 67 107 240 212 299 318 70 112 232 211 0 0 77 71 21 36 100 100 100 100 452 443 1.132 .883 .909 .997 .837 .543 52 314 .737 .82 80 4070 19920 72 80 319 327 0 285 96 189 .789 284 188 1.268 .812 -.342 -.3 -.3
16 622 556 64 108 558 448 631 571 70 113 567 463 0 0 195 188 35 41 100 98 98 94 1006 1030 1.246 .803 .817 .835 .829 .309 52 283 .732 .89 80 4230 19920 72 80 335 343 0 496 96 400 .717 510 413 1.395 .729 -.48 -.456 -.456
17 11573 17721 65 107 11508 17614 12537 19122 69 111 12472 19015 0 0 2607 4856 28 34 100 100 100 100 29122 31487 .653 1.531 1.525 1.525 1.566 .266 52 279 1.521 .98 80 4390 19910 71 79 351 359 0 15822 96 15727 1.367 17073 16978 .732 1.361 .451 .445 .445
18 1115 1091 64 103 1051 988 1265 1194 69 107 1201 1091 0 0 473 476 32 34 100 100 100 100 2039 2292 1.064 .94 .908 .999 .968 .448 80 429 .92 .96 100 4550 19910 70 80 366 376 0 974 92 882 .839 1066 974 1.191 .811 -.253 -.302 -.302
19 2888 1969 60 95 2828 1874 3303 2233 68 100 3243 2138 0 0 1181 869 38 35 100 100 100 100 4702 5381 1.509 .663 .659 .651 .653 .181 80 400 .643 .96 100 4720 19900 69 79 383 393 0 1758 85 1673 .592 1994 1909 1.69 .589 -.757 -.765 -.765
20 1797 2398 57 93 1740 2305 1877 2367 61 97 1820 2274 0 0 350 344 18 30 100 100 100 100 4045 4094 .755 1.325 1.249 1.427 1.298 .677 52 313 1.217 .96 90 4870 19900 69 78 398 407 0 2141 83 2058 1.183 2113 2030 .845 1.116 .242 .158 .158

Total number of rows: 21888

Table truncated, full table size 4997 Kbytes.




Supplementary data files not provided
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