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Sample GSM130500 Query DataSets for GSM130500
Status Public on Aug 25, 2006
Title 100-55.1_D_digit1and2
Sample type RNA
 
Channel 1
Source name Amplifiied Human Universal Reference
Organism Homo sapiens
Characteristics Amplifiied Human Universal Reference
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name Poly A RNA L hand, dorsal, lateral (V of digit 1 and 2)
Organism Homo sapiens
Characteristics Poly A RNA L hand, dorsal, lateral (V of digit 1 and 2)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Skin, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59471.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 Aug 24, 2006
Last update date Aug 24, 2006
Contact name Howard Chang
E-mail(s) [email protected]
Fax 650-723-8762
Organization name Stanford University
Department Dermatology
Street address CCSR 2142
City Stanford
State/province CA
Country USA
 
Platform ID GPL4214
Series (1)
GSE5591 Anatomic demarcation by positional variation in fibroblast gene expression programs.

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 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
1 637 559 394 780 243 -221 684 489 406 805 290 -291 0 0 176 230 84 159 75 3 63 3 22 -1 null null null .878 .8 1.809 52 312 -1.463 -.62 80 1590 5380 78 86 35 43 -50 1028 1434 -406 null 899 -535 null null null null
2 4409 499 392 823 4017 -324 5025 445 411 847 4633 -378 0 0 2034 228 86 175 94 3 88 0 3693 4255 null null null 1.424 1.466 1.41 52 338 -.085 -.75 90 1750 5380 77 86 50 59 0 918 1513 -596 null 818 -695 null null null null
3 1794 957 400 804 1394 153 1851 966 426 825 1451 162 0 0 721 134 127 153 93 53 90 12 1547 1613 9.111 .11 .112 .112 .118 4.015 32 206 .07 .36 70 1890 5380 78 85 65 72 0 1760 1478 281 .202 1776 298 4.955 .205 -2.309 -2.284
4 1234 676 401 848 833 -172 1141 653 407 863 740 -195 0 0 862 230 83 169 76 7 73 1 661 545 null null null .73 1.025 6.011 52 285 -.029 -.09 80 2030 5380 78 86 79 87 -50 1243 1559 -316 null 1201 -359 null null null null
5 1131 1558 410 905 721 653 1155 1540 424 925 745 635 0 0 407 377 92 202 90 88 86 73 1374 1380 1.104 .906 .852 1 .933 2.137 52 301 .969 .9 90 2180 5380 77 86 93 102 0 2865 1664 1201 1.665 2832 1168 .6 1.567 .736 .648
6 516 742 399 894 117 -152 516 775 413 930 117 -119 0 0 130 291 104 215 53 9 25 1 -35 -2 null null null 3.692 2.924 2.879 52 282 -9.186 -.19 80 2320 5380 78 86 108 116 -50 1364 1644 -279 null 1425 -219 null null null null
7 850 1072 410 940 440 132 912 1021 431 989 502 81 0 0 371 206 121 275 71 26 59 1 572 583 3.333 .3 .161 .448 .446 5.06 52 272 .451 .39 80 2470 5380 78 86 123 131 -50 1971 1728 243 .552 1877 149 1.813 .297 -.858 -1.753
8 619 1081 421 950 198 131 591 1027 434 977 170 77 0 0 211 278 115 234 59 32 42 9 329 247 1.511 .662 .453 .763 .787 2.822 52 254 1.359 .65 80 2610 5380 78 86 137 145 -50 1988 1747 241 1.217 1888 142 .822 .833 .283 -.264
9 1322 901 437 968 885 -67 1436 853 460 1017 999 -115 0 0 446 187 133 259 91 5 85 1 818 884 null null null .265 .204 6.736 80 358 -.081 -.2 100 2760 5380 77 87 151 161 0 1657 1780 -123 null 1568 -211 null null null null
10 1959 837 446 935 1513 -98 1945 811 481 986 1499 -124 0 0 330 191 164 232 100 5 100 3 1415 1375 null null null .054 .039 2.881 52 264 -.114 -.32 90 2900 5390 78 87 165 174 0 1539 1719 -180 null 1491 -228 null null null null
11 2238 9851 445 979 1793 8872 2486 11271 552 1028 2041 10292 0 0 903 4116 894 298 81 92 62 91 10665 12333 .202 4.948 5.043 4.73 4.973 1.582 80 347 4.871 .98 100 3050 5390 78 88 180 190 0 18114 1800 16314 9.099 20725 18925 .11 9.272 3.186 3.213
12 11814 15349 438 973 11376 14376 13321 17065 483 1028 12883 16092 0 0 4891 5950 297 275 98 98 92 98 25752 28975 .791 1.264 1.249 1.368 1.288 1.346 80 335 1.242 .99 100 3200 5390 78 88 195 205 0 28223 1789 26434 2.324 31379 29590 .43 2.297 1.216 1.2
13 3171 5332 449 1019 2722 4313 3672 6010 482 1099 3223 4991 0 0 1248 1925 140 322 90 90 88 88 7035 8214 .631 1.584 1.549 1.706 1.578 1.431 80 362 1.563 .99 100 3350 5380 77 87 210 220 0 9804 1874 7931 2.914 11051 9177 .343 2.847 1.543 1.51
14 885 837 458 1011 427 -174 857 789 499 1072 399 -222 0 0 224 326 189 413 86 1 50 1 253 177 null null null .335 .317 6.787 52 242 4.978 .04 80 3490 5380 78 86 225 233 -50 1539 1859 -320 null 1451 -408 null null null null
15 1026 1127 467 1012 559 115 1025 1115 532 1076 558 103 0 0 206 260 221 423 96 11 67 0 674 661 4.861 .206 .185 .314 .365 2.69 52 244 1.768 .45 80 3630 5390 79 87 239 247 0 2072 1861 211 .378 2050 189 2.644 .339 -1.402 -1.559
16 10686 4962 480 1104 10206 3858 13065 5849 574 1164 12585 4745 0 0 5832 2145 625 353 82 85 82 83 14064 17330 2.645 .378 .377 .473 .387 1.933 80 414 .371 .99 110 3780 5380 76 87 252 263 0 9124 2030 7094 .695 10755 8725 1.439 .693 -.525 -.528
17 4829 6363 453 1053 4376 5310 5751 7456 555 1111 5298 6403 0 0 2415 2842 670 327 81 90 81 85 9686 11701 .824 1.213 1.209 1.482 1.236 1.881 80 360 1.19 .98 100 3930 5380 77 87 268 278 0 11700 1936 9764 2.231 13710 11774 .448 2.222 1.158 1.152
18 1529 956 432 968 1097 -12 1617 885 473 1007 1185 -83 0 0 403 337 187 230 96 3 90 3 1085 1102 null null null .069 .116 7.425 52 242 -.015 -.03 80 4080 5380 78 86 284 292 0 1758 1780 -22 null 1627 -153 null null null null
19 7456 4033 447 1016 7009 3017 8912 4535 510 1081 8465 3519 0 0 3753 1515 336 319 85 88 82 82 10026 11984 2.323 .43 .416 .579 .437 2.418 80 347 .412 .98 100 4220 5380 77 87 297 307 0 7416 1868 5548 .791 8339 6471 1.263 .764 -.337 -.388
20 7603 7369 461 1101 7142 6268 9134 8399 584 1227 8673 7298 0 0 3440 2924 532 502 87 92 86 87 13410 15971 1.139 .878 .841 1.046 .878 2.034 80 410 .86 .98 110 4360 5380 76 87 310 321 0 13550 2024 11525 1.614 15444 13419 .62 1.547 .69 .63

Total number of rows: 41472

Table truncated, full table size 9256 Kbytes.




Supplementary data files not provided
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