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Sample GSM39894 Query DataSets for GSM39894
Status Public on Feb 21, 2005
Title Vagina 0304
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Vagina 0304
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-03/26263.gif
 
Submission date Jan 26, 2005
Last update date Nov 22, 2005
Contact name Jonathan Pollack
E-mail(s) [email protected]
Phone 650-736-1987
Organization name Stanford University
Department Pathology
Lab Pollack Lab
Street address 269 Campus Drive, CCSR3245A
City Stanford
State/province CA
ZIP/Postal code 94305-5176
Country USA
 
Platform ID GPL1823
Series (1)
GSE2193 Normal_human_tissues

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
VALUE same as UNF_VALUE but with flagged values removed
LOG_RAT2N_MEDIAN 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
UNF_VALUE 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

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 VALUE LOG_RAT2N_MEDIAN UNF_VALUE
1 278 256 131 169 147 87 288 242 128 172 157 73 0 0 85 73 33 36 84 84 81 50 234 230 1.69 .592 .465 .668 .417 4.285 32 151 .508 .4 60 1600 7260 43 49 33 39 0 235 155 80 .543 222 67 1.842 .427 -.881 -1.229 -.881
2 185 154 130 176 55 -22 187 142 130 178 57 -34 0 0 64 42 33 35 57 10 46 1 33 23 null null null .653 .62 4.319 80 411 2.627 .23 100 1730 7250 40 50 44 54 -50 141 161 -20 null 130 null null null null null
3 608 1537 129 163 479 1374 647 1597 130 167 518 1434 0 0 185 464 33 37 100 100 98 100 1853 1952 .349 2.868 2.768 3.063 2.78 1.694 52 345 3.143 .89 90 1900 7250 40 49 61 70 0 1410 150 1261 2.632 1465 1316 .38 2.54 1.396 1.345 1.396
4 2125 2620 123 152 2002 2468 2242 2558 127 161 2119 2406 0 0 859 1105 36 63 100 100 100 100 4470 4525 .811 1.233 1.135 1.276 1.251 1.904 52 316 1.299 .9 90 2040 7250 40 49 75 84 0 2404 139 2264 1.131 2347 2207 .884 1.042 .178 .059 .178
5 355 1402 124 153 231 1249 378 1317 124 159 254 1164 0 0 105 577 30 40 93 100 90 100 1480 1418 .185 5.407 4.583 5.661 5.163 1.777 32 194 5.712 .87 70 2180 7250 41 48 90 97 0 1286 140 1146 4.96 1208 1068 .202 4.204 2.31 2.072 2.31
6 184 176 126 166 58 10 172 173 126 172 46 7 0 0 77 37 30 38 56 16 46 5 68 53 5.8 .172 .152 .394 .435 4.024 80 365 -1 -1 100 2310 7250 40 50 102 112 -50 161 152 9 .158 159 6 6.322 .14 -2.841 -2.66
7 184 7547 121 163 63 7384 184 8414 122 164 63 8251 0 0 57 3455 31 36 68 100 50 100 7447 8314 .009 117.206 130.968 67.959 72.091 1.34 80 336 116.198 .67 100 2480 7250 40 50 119 129 0 6924 150 6774 107.529 7719 7570 .009 120.154 6.749 6.909 6.749
8 1712 2573 122 159 1590 2414 1818 2826 123 161 1696 2667 0 0 635 919 31 34 100 100 100 100 4004 4363 .659 1.518 1.573 1.667 1.527 2.034 52 265 1.621 .9 90 2620 7250 40 49 133 142 0 2361 146 2215 1.393 2593 2447 .718 1.443 .478 .529 .478
9 420 1428 122 163 298 1265 469 1516 124 161 347 1353 0 0 168 271 29 32 90 100 86 100 1563 1700 .236 4.245 3.899 4.668 3.879 1.959 52 245 4.074 .87 80 2760 7260 42 50 148 156 0 1310 150 1161 3.894 1391 1241 .257 3.577 1.961 1.839 1.961
10 262 247 120 156 142 91 278 246 124 157 158 90 0 0 78 41 31 32 87 93 84 68 233 248 1.56 .641 .57 .505 .54 2.044 32 219 .522 .52 70 2900 7250 41 48 162 169 0 227 143 83 .588 226 83 1.701 .523 -.766 -.936 -.766
11 522 619 122 161 400 458 512 641 125 161 390 480 0 0 179 170 32 35 96 100 96 100 858 870 .873 1.145 1.231 1.18 1.264 1.637 52 273 1.143 .9 80 3060 7250 41 49 178 186 0 568 148 420 1.05 588 440 .952 1.129 .071 .175 .071
12 629 418 121 156 508 262 652 431 123 158 531 275 0 0 194 93 30 34 94 100 94 96 770 806 1.939 .516 .518 .492 .473 1.768 52 244 .469 .84 80 3200 7250 41 49 192 200 0 383 143 240 .473 395 252 2.113 .475 -1.08 -1.074 -1.08
13 403 354 120 160 283 194 416 359 128 164 296 199 0 0 137 109 44 41 92 90 90 78 477 495 1.459 .686 .672 .588 .691 2.326 52 264 .708 .83 80 3340 7250 41 49 206 214 0 325 147 178 .629 329 183 1.59 .617 -.669 -.697 -.669
14 259 148 121 157 138 -9 269 142 122 158 148 -15 0 0 67 35 29 33 90 12 90 3 129 133 null null null .14 .149 2.826 32 152 11.071 .19 60 3490 7250 42 48 222 228 0 136 144 -8 null 130 null null null null null null
15 1416 1358 126 160 1290 1198 1548 1522 126 164 1422 1362 0 0 749 465 29 35 92 100 91 100 2488 2784 1.077 .929 .958 1.181 .983 2.604 80 348 .824 .9 100 3630 7250 40 50 234 244 0 1246 147 1099 .852 1396 1250 1.174 .879 -.231 -.187 -.231
16 874 877 125 161 749 716 967 901 124 164 842 740 0 0 298 247 29 35 92 100 92 96 1465 1582 1.046 .956 .879 1.012 .948 1.814 52 278 .938 .92 90 3780 7240 39 48 249 258 0 805 148 657 .877 827 679 1.14 .806 -.189 -.311 -.189
17 180 158 124 165 56 -7 186 152 125 167 62 -13 0 0 61 34 29 35 62 10 52 2 49 49 null null null .433 .432 4.982 80 339 -1 -1 100 3920 7240 39 49 263 273 -50 145 151 -6 null 139 null null null null null
18 165 147 123 161 42 -14 154 146 125 164 31 -15 0 0 64 32 31 35 48 10 32 0 28 16 null null null .561 .647 3.356 80 379 5.084 .09 100 4060 7240 39 49 277 287 -50 135 148 -13 null 134 null null null null null
19 457 330 126 153 331 177 521 319 138 151 395 166 0 0 209 84 54 35 83 100 83 100 508 561 1.87 .535 .42 .415 .44 1.763 12 104 .478 .69 50 4210 7250 42 47 294 299 0 303 140 162 .491 293 152 2.038 .386 -1.027 -1.375 -1.027
20 224 162 123 153 101 9 248 158 125 156 125 5 0 0 69 30 30 34 87 21 81 3 110 130 11.222 .089 .04 .216 .307 2.922 32 196 .124 .16 70 4370 7250 41 48 309 316 0 149 140 8 .082 145 5 12.232 .037 -3.613 -4.768 -3.613

Total number of rows: 43008

Table truncated, full table size 9269 Kbytes.




Supplementary data files not provided
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