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Sample GSM88436 Query DataSets for GSM88436
Status Public on Dec 21, 2005
Title N-58, NORM, M, GSF, 6 x ETOH, 14d
Sample type RNA
 
Channel 1
Source name mixed reference (FR + CRG)
Organism Homo sapiens
Characteristics mixed reference (FR + CRG)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name nGSF58, G0, 6 x ETOH, 14 days
Organism Homo sapiens
Characteristics nGSF58, G0, 6 x ETOH, 14 days
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17292.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 Dec 19, 2005
Last update date Sep 22, 2006
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 GPL3039
Series (2)
GSE3871 Effects of androgen treatment on genital fibroblasts
GSE4353 Genital fibroblasts of normal males and 46,XY females with androgen insensitivity syndrome

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
1 251 245 245 492 6 -247 248 165 255 552 3 -327 0 0 73 163 67 291 15 0 1 0 -241 -324 null null null 4.577 5.88 3.869 120 535 14.86 .24 120 1480 8850 47 59 50 62 -100 250 502 -252 null 168 -333 null null null null
2 272 292 247 278 25 14 256 228 251 294 9 -50 0 0 89 202 53 132 30 19 14 12 39 -41 1.786 .56 null 2.306 2.625 3.972 120 344 5.508 .37 120 1620 8850 47 59 64 76 -100 298 283 14 .571 232 -51 1.751 null -.809 null
3 928 679 254 185 674 494 949 679 256 191 695 494 0 0 233 146 52 63 95 100 93 100 1168 1189 1.364 .733 .711 .787 .756 2.108 80 212 .888 .84 100 1760 8860 49 59 79 89 0 692 189 504 .747 692 504 1.338 .725 -.42 -.465
4 273 198 251 158 22 40 249 148 251 161 -2 -10 0 0 102 174 54 47 21 20 13 13 62 -12 .55 1.818 null 1.066 1.164 4.43 120 385 2.823 .54 120 1890 8850 47 59 91 103 -100 202 161 41 1.854 151 -10 .539 null .89 null
5 925 1680 243 134 682 1546 962 1693 243 138 719 1559 0 0 194 307 54 39 100 100 100 100 2228 2278 .441 2.267 2.168 2.339 2.218 1.511 80 261 2.474 .88 100 2030 8850 48 58 106 116 0 1713 137 1576 2.311 1726 1590 .433 2.211 1.209 1.145
6 255 138 229 114 26 24 234 109 233 122 5 -5 0 0 81 92 48 47 31 19 16 15 50 0 1.083 .923 null .876 .985 3.212 120 386 2.49 .4 120 2160 8850 47 59 118 130 -100 141 116 24 .941 111 -5 1.063 null -.088 null
7 724 986 227 96 497 890 737 999 229 99 510 903 0 0 165 207 49 29 97 100 97 100 1387 1413 .558 1.791 1.771 1.911 1.725 1.879 80 252 2.041 .84 100 2300 8850 48 58 133 143 0 1005 98 907 1.826 1019 921 .548 1.805 .869 .852
8 915 1248 240 117 675 1131 952 1253 244 131 712 1136 0 0 271 238 60 111 93 100 93 98 1806 1848 .597 1.676 1.596 1.722 1.637 1.744 80 331 1.768 .86 110 2430 8850 47 58 145 156 0 1272 119 1153 1.708 1278 1158 .585 1.627 .773 .702
9 724 561 265 132 459 429 760 563 281 171 495 431 0 0 196 158 76 176 96 100 90 68 888 926 1.07 .935 .871 1.009 .868 2.125 32 134 1.688 .56 70 2570 8870 51 58 161 168 0 572 135 437 .953 574 439 1.049 .888 -.07 -.172
10 331 145 281 226 50 -81 323 124 284 220 42 -102 0 0 74 74 61 88 41 4 13 0 -31 -60 null null null 2.675 3.171 3.581 120 386 9.213 .16 120 2700 8850 47 59 172 184 0 148 230 -83 null 126 -104 null null null null
11 883 112 263 147 620 -35 877 109 262 156 614 -38 0 0 147 29 50 57 100 1 100 0 585 576 null null null .062 .055 1.652 80 207 -1.175 -.1 100 2840 8850 48 58 187 197 0 114 150 -36 null 111 -39 null null null null
12 268 155 230 117 38 38 245 146 236 125 15 29 0 0 74 74 52 51 39 36 20 16 76 44 1 1 1.933 1.046 1.065 3.461 120 367 2.828 .35 120 2980 8840 46 58 200 212 0 158 119 39 1.02 149 30 .981 1.971 .028 .979
13 431 257 244 114 187 143 439 249 244 127 195 135 0 0 78 77 51 60 96 90 88 61 330 330 1.308 .765 .692 .746 .682 2.4 52 227 1.319 .64 90 3110 8840 47 56 214 223 0 262 116 146 .78 254 138 1.283 .706 -.359 -.503
14 471 353 250 125 221 228 481 329 253 133 231 204 0 0 99 123 55 47 95 100 83 96 449 435 .969 1.032 .883 1.05 .995 1.92 80 286 1.627 .64 110 3250 8850 47 58 227 238 0 360 127 232 1.052 335 208 .951 .9 .073 -.151
15 291 208 263 156 28 52 277 164 267 163 14 8 0 0 85 169 57 59 29 25 12 13 80 22 .538 1.857 .571 .721 .707 3.995 120 410 4.779 .33 120 3380 8840 46 58 240 252 -100 212 159 53 1.893 167 8 .528 .583 .921 -.779
16 473 1617 262 179 211 1438 398 1283 271 184 136 1104 0 0 208 1266 55 44 78 100 53 100 1649 1240 .147 6.815 8.118 7.584 6.356 2.702 32 105 7.575 .82 60 3540 8820 47 53 259 265 -100 1649 183 1466 6.949 1308 1126 .144 8.276 2.797 3.049
17 277 174 250 123 27 51 274 144 258 132 24 21 0 0 55 89 57 54 30 30 5 19 78 45 .529 1.889 .875 1.003 1.167 5.143 120 434 5.861 .22 120 3660 8840 46 58 268 280 0 177 125 52 1.926 147 21 .519 .892 .945 -.165
18 417 533 247 100 170 433 423 558 252 107 176 458 0 0 74 128 53 54 92 98 82 97 603 634 .393 2.547 2.602 2.52 2.348 1.769 80 275 2.961 .75 100 3800 8840 47 57 283 293 0 543 102 441 2.597 569 467 .385 2.653 1.377 1.408
19 404 285 247 93 157 192 407 271 249 95 160 178 0 0 89 89 52 27 90 100 68 100 349 338 .818 1.223 1.113 1.312 1.187 2.052 80 264 1.553 .68 100 3940 8850 48 58 297 307 0 291 95 196 1.247 276 181 .802 1.134 .318 .182
20 1002 779 250 96 752 683 1012 786 250 113 762 690 0 0 177 296 52 98 100 97 100 92 1435 1452 1.101 .908 .906 .815 .856 1.696 80 232 1.242 .83 100 4080 8840 47 57 311 321 0 794 98 696 .926 801 704 1.08 .923 -.111 -.115

Total number of rows: 44544

Table truncated, full table size 9385 Kbytes.




Supplementary data files not provided
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