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Sample GSM62238 Query DataSets for GSM62238
Status Public on Jun 25, 2005
Title hif-1 2N vs. hif-1 2H
Sample type RNA
 
Channel 1
Source name hif-1 2H
Organism Caenorhabditis elegans
Characteristics hif-1 2H
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name hif-1 2N
Organism Caenorhabditis elegans
Characteristics hif-1 2N
Extracted molecule total RNA
Label Cy5
 
 
Description Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-03/27036.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) mjiang@cmgm.stanford.edu
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 12045 7685 63 168 11982 7517 11639 7861 69 175 11576 7693 0 0 4799 2464 37 72 100 100 100 100 19499 19269 1.594 .627 .665 .718 .618 .41 80 394 .57 .94 100 1820 19850 64 74 93 103 0 12598 275 12323 1.028 12887 12611 .972 1.089 .04 .124 .124
2 6103 2798 62 166 6041 2632 6248 2700 65 177 6186 2534 0 0 1670 921 21 76 100 100 100 100 8673 8720 2.295 .436 .41 .447 .43 .133 52 349 .411 .92 90 1990 19850 64 73 110 119 0 4587 272 4315 .714 4426 4154 1.4 .672 -.486 -.574 -.574
3 286 327 61 170 225 157 282 325 69 179 221 155 0 0 66 96 31 80 100 84 100 43 382 376 1.433 .698 .701 .829 .707 .516 32 220 .469 .46 70 2140 19850 65 72 126 133 0 536 279 257 1.144 533 254 .874 1.15 .194 .201 .201
4 1544 703 66 172 1478 531 1583 708 72 181 1517 536 0 0 535 293 31 76 100 96 100 90 2009 2053 2.783 .359 .353 .366 .354 .174 52 294 .355 .85 80 2300 19860 66 74 142 150 0 1152 282 870 .589 1161 879 1.698 .579 -.764 -.788 -.788
5 10943 2625 67 163 10876 2462 12024 2808 77 176 11957 2645 0 0 4052 845 37 84 100 100 100 100 13338 14602 4.418 .226 .221 .248 .227 .112 52 374 .2 .94 90 2470 19840 63 72 158 167 0 4303 267 4036 .371 4603 4336 2.695 .363 -1.43 -1.463 -1.463
6 3288 1308 71 180 3217 1128 2820 1246 93 190 2749 1066 0 0 2022 671 67 81 100 100 100 91 4345 3815 2.852 .351 .388 .409 .361 .225 12 98 .314 .88 50 2620 19850 66 71 175 180 0 2144 295 1849 .575 2043 1748 1.74 .636 -.799 -.654 -.654
7 13095 5008 66 172 13029 4836 12575 5078 71 178 12509 4906 0 0 6156 2872 26 73 100 100 100 100 17865 17415 2.694 .371 .392 .352 .358 .132 52 390 .381 .97 90 2800 19860 65 74 191 200 0 8210 282 7928 .608 8325 8043 1.643 .643 -.717 -.637 -.637
8 424 351 66 169 358 182 394 331 69 179 328 162 0 0 223 120 20 80 100 81 96 50 540 490 1.967 .508 .494 .727 .572 .608 32 160 .43 .69 60 2960 19850 66 72 209 215 0 575 277 298 .833 543 266 1.2 .81 -.263 -.305 -.305
9 7000 972 66 169 6934 803 7048 974 70 175 6982 805 0 0 1811 236 35 75 100 100 100 100 7737 7787 8.635 .116 .115 .153 .117 .283 80 435 .106 .9 100 3120 19850 64 74 223 233 0 1593 277 1316 .19 1597 1320 5.267 .189 -2.397 -2.403 -2.403
10 434 427 69 162 365 265 408 434 192 207 339 272 0 0 116 126 1367 404 0 11 0 0 630 611 1.377 .726 .802 .79 .732 .438 52 294 .24 .5 80 3280 19870 67 75 240 248 0 700 266 434 1.19 711 446 .84 1.315 .251 .395 .395
11 8901 1351 63 171 8838 1180 9019 1422 146 201 8956 1251 0 0 1837 368 1117 333 100 100 100 90 10018 10207 7.49 .134 .14 .135 .138 .039 80 441 .132 .83 100 3440 19850 64 74 255 265 0 2215 280 1934 .219 2331 2051 4.569 .229 -2.192 -2.127 -2.127
12 380 543 62 171 318 372 383 513 66 174 321 342 0 0 71 162 22 75 100 100 100 96 690 663 .855 1.17 1.065 1.207 1.157 .548 52 358 .997 .75 90 3610 19850 64 73 272 281 0 890 280 610 1.918 841 561 .521 1.747 .939 .805 .805
13 7041 1388 64 168 6977 1220 7114 1384 88 176 7050 1216 0 0 1983 426 145 80 100 100 100 100 8197 8266 5.719 .175 .172 .178 .167 .059 52 369 .166 .92 90 3760 19850 64 73 287 296 0 2275 275 2000 .287 2269 1993 3.489 .283 -1.803 -1.822 -1.822
14 245 328 68 190 177 138 244 309 384 531 176 119 0 0 60 152 1216 1256 0 0 0 0 315 295 1.283 .78 .676 1.057 .85 .848 32 170 .949 .6 60 3920 19860 67 73 305 311 0 538 311 226 1.278 507 195 .782 1.108 .354 .149 .149
15 301 261 67 184 234 77 309 260 577 629 242 76 0 0 118 112 1931 1614 0 0 0 0 311 318 3.039 .329 .314 .945 .574 1.71 52 300 .674 .94 80 4100 19850 65 73 322 330 0 428 302 126 .539 426 125 1.854 .515 -.89 -.958 -.958
16 490 336 72 171 418 165 494 292 76 182 422 121 0 0 111 140 29 81 100 71 100 43 583 543 2.533 .395 .287 .531 .451 .47 32 218 .295 .5 70 4240 19850 65 72 336 343 0 551 280 270 .647 479 198 1.545 .47 -.628 -1.089 -1.089
17 7455 2184 67 174 7388 2010 7961 2313 173 282 7894 2139 0 0 2608 951 661 547 100 90 100 80 9398 10033 3.676 .272 .271 .27 .294 .092 52 310 .272 .94 80 4410 19860 66 74 353 361 0 3580 285 3295 .446 3792 3507 2.242 .444 -1.165 -1.171 -1.171
18 1412 895 63 173 1349 722 1377 881 66 188 1314 708 0 0 210 171 18 85 100 100 100 100 2071 2022 1.868 .535 .539 .545 .533 .141 52 297 .497 .9 80 4560 19860 66 74 368 376 0 1467 284 1184 .877 1444 1161 1.14 .883 -.189 -.179 -.179
19 2198 586 60 169 2138 417 2252 584 63 179 2192 415 0 0 505 193 19 73 100 95 100 90 2555 2607 5.127 .195 .189 .205 .202 .114 80 441 .187 .86 100 4730 19850 64 74 384 394 0 961 277 684 .32 957 680 3.128 .31 -1.645 -1.688 -1.688
20 1272 888 58 167 1214 721 1166 847 62 178 1108 680 0 0 659 299 19 76 100 100 100 100 1935 1788 1.684 .594 .614 .626 .643 .207 52 352 .47 .86 90 4890 19860 65 74 400 409 0 1456 274 1182 .974 1389 1115 1.027 1.006 -.039 .009 .009

Total number of rows: 21888

Table truncated, full table size 4945 Kbytes.




Supplementary data files not provided
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