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Sample GSM88424 Query DataSets for GSM88424
Status Public on Dec 21, 2005
Title N-33, NORM, M, GSF, 6 x ETOH, 14d
Sample type RNA
 
Channel 1
Source name mixed reference (CRG + FR)
Organism Homo sapiens
Characteristics mixed reference (CRG + FR)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name nGSF33, G0, 6 x ETOH, 14 days
Organism Homo sapiens
Characteristics nGSF33, G0, 6 x ETOH, 14 days
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15601.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
1 596 509 231 148 365 361 623 490 235 151 392 342 0 0 139 229 55 57 98 88 94 84 726 734 1.011 .989 .872 .958 .976 2.098 52 305 1.608 .74 90 1790 9130 48 57 30 39 0 467 136 331 .908 450 314 1.102 .801 -.14 -.321
2 677 648 214 119 463 529 735 692 220 126 521 573 0 0 323 333 54 51 84 96 78 84 992 1094 .875 1.143 1.1 1.209 1.046 4.03 32 100 1.876 .57 60 1930 9160 53 59 46 52 0 595 109 485 1.049 635 526 .954 1.009 .068 .013
3 1629 1563 234 131 1395 1432 1606 1572 238 138 1372 1441 0 0 382 370 56 53 100 100 100 100 2827 2813 .974 1.027 1.05 1.023 1.06 1.47 80 331 1.148 .88 110 2050 9130 47 58 55 66 0 1434 120 1314 .942 1443 1322 1.061 .964 -.086 -.053
4 514 450 228 137 286 313 426 429 229 144 198 292 0 0 260 288 50 52 81 78 71 75 599 490 .914 1.094 1.475 1.099 .888 3.841 32 100 1.941 .56 60 2170 9140 51 57 70 76 0 413 126 287 1.004 394 268 .996 1.353 .006 .437
5 1132 2575 233 128 899 2447 1143 2578 238 137 910 2450 0 0 322 499 54 65 98 100 93 100 3346 3360 .367 2.722 2.692 2.962 2.66 1.773 80 373 2.791 .87 110 2310 9120 46 57 81 92 0 2363 117 2246 2.498 2366 2248 .4 2.471 1.321 1.305
6 526 447 227 110 299 337 498 495 228 116 271 385 0 0 246 282 47 51 71 71 68 65 636 656 .887 1.127 1.421 .97 1.165 3.516 32 115 1.511 .75 60 2450 9130 50 56 98 104 0 410 101 309 1.034 454 353 .967 1.304 .049 .383
7 1117 1636 227 121 890 1515 1119 1574 233 133 892 1453 0 0 349 497 52 57 100 100 100 100 2405 2345 .587 1.702 1.629 1.739 1.766 1.629 80 279 1.816 .89 100 2580 9120 47 57 109 119 0 1501 111 1390 1.562 1445 1333 .64 1.495 .644 .58
8 1249 1298 242 135 1007 1163 1259 1291 243 144 1017 1156 0 0 267 309 57 65 100 100 100 100 2170 2173 .866 1.155 1.137 1.156 1.137 1.449 80 346 1.268 .89 110 2710 9120 46 57 121 132 0 1191 124 1067 1.06 1185 1061 .943 1.043 .084 .061
9 1091 752 256 131 835 621 1098 723 259 137 842 592 0 0 374 258 62 59 96 96 96 96 1456 1434 1.345 .744 .703 .771 .701 2.511 32 173 .979 .77 70 2870 9120 48 55 139 146 0 690 120 570 .683 664 543 1.465 .645 -.551 -.632
10 511 415 247 137 264 278 490 392 250 140 243 255 0 0 122 159 60 53 98 97 87 90 542 498 .95 1.053 1.049 1.01 1.116 2.099 80 274 1.877 .62 100 2990 9110 46 56 150 160 0 381 126 255 .966 360 234 1.035 .963 -.049 -.054
11 1184 251 236 128 948 123 1220 245 239 133 984 117 0 0 254 91 55 57 100 76 100 51 1071 1101 7.707 .13 .119 .118 .127 2.338 80 266 .353 .56 110 3120 9120 46 57 162 173 0 230 117 113 .119 225 107 8.398 .109 -3.07 -3.196
12 953 1016 236 128 717 888 952 980 243 134 716 852 0 0 275 301 50 54 97 100 97 100 1605 1568 .807 1.238 1.19 1.339 1.298 1.844 80 289 1.367 .87 110 3260 9120 46 57 176 187 0 932 117 815 1.137 899 782 .88 1.092 .185 .127
13 526 398 245 146 281 252 523 398 248 146 278 252 0 0 88 101 55 53 100 98 98 92 533 530 1.115 .897 .906 .866 .88 1.751 52 235 1.463 .63 90 3390 9110 46 55 190 199 0 365 134 231 .823 365 231 1.215 .832 -.281 -.265
14 761 683 258 140 503 543 753 700 265 142 495 560 0 0 158 184 57 53 100 100 100 98 1046 1055 .926 1.08 1.131 1.056 1.099 1.581 80 280 1.322 .82 100 3530 9110 46 56 204 214 0 627 128 498 .991 642 514 1.009 1.038 -.013 .054
15 1042 913 266 145 776 768 1016 930 277 155 750 785 0 0 198 337 73 80 100 96 100 92 1544 1535 1.01 .99 1.047 .95 1.08 1.676 52 232 1.265 .86 90 3650 9110 46 55 216 225 0 838 133 705 .908 854 720 1.101 .961 -.139 -.058
16 1036 596 258 142 778 454 1047 610 271 158 789 468 0 0 147 160 81 87 100 98 100 94 1232 1257 1.714 .584 .593 .546 .589 1.55 52 264 .788 .83 90 3790 9100 45 54 230 239 0 547 130 417 .536 560 430 1.867 .544 -.901 -.877
17 729 647 274 138 455 509 749 633 283 149 475 495 0 0 146 173 71 71 100 100 96 98 964 970 .894 1.119 1.042 1.128 1.139 1.603 80 278 1.377 .84 100 3940 9110 46 56 245 255 0 594 127 467 1.027 581 454 .974 .956 .038 -.064
18 458 423 267 138 191 285 449 412 273 146 182 274 0 0 96 123 60 63 95 97 77 87 476 456 .67 1.492 1.505 1.573 1.527 2.201 80 280 2.207 .64 100 4070 9110 46 56 258 268 0 388 127 262 1.369 378 251 .73 1.382 .454 .466
19 471 311 277 143 194 168 477 303 279 149 200 160 0 0 86 92 58 64 94 88 82 61 362 360 1.155 .866 .8 .879 .763 2.244 52 271 1.821 .56 90 4220 9100 45 54 273 282 0 285 131 154 .795 278 147 1.258 .734 -.331 -.446
20 1018 938 290 143 728 795 1051 1021 291 151 761 878 0 0 218 337 60 64 100 97 100 93 1523 1639 .916 1.092 1.154 1.025 1.088 1.921 80 256 1.385 .84 100 4360 9110 46 56 287 297 0 861 131 730 1.002 937 806 .998 1.059 .003 .082

Total number of rows: 44544

Table truncated, full table size 9609 Kbytes.




Supplementary data files not provided
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