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Sample GSM39952 Query DataSets for GSM39952
Status Public on Feb 21, 2005
Title Uterus, endomyometrium 0158
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Uterus, endomyometrium 0158
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-05/28323.gif
 
Submission date Jan 26, 2005
Last update date Nov 22, 2005
Contact name Jonathan Pollack
E-mail(s) pollack1@stanford.edu
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 GPL1824
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
1 101 214 65 34 36 180 101 220 68 37 36 186 0 0 34 88 17 13 75 98 50 92 216 222 .2 5 5.167 5.16 5.311 2.08 52 381 4.965 .68 90 1610 8040 55 64 56 65 0 181 29 153 4.237 186 158 .236 4.379 2.083 2.13 2.083
2 105 63 67 32 38 31 108 59 71 35 41 27 0 0 46 20 20 13 65 78 53 50 69 68 1.226 .816 .659 .534 .545 2.026 32 146 .358 .53 60 1790 8040 57 63 76 82 0 53 27 26 .691 50 23 1.446 .558 -.533 -.841 -.533
3 219 539 67 32 152 507 231 576 68 33 164 544 0 0 78 196 17 9 92 100 91 100 659 708 .3 3.336 3.317 3.535 3.403 1.96 80 331 3.471 .85 100 1910 8040 55 65 86 96 0 457 27 430 2.827 488 461 .354 2.811 1.499 1.491 1.499
4 614 1085 68 35 546 1050 553 1188 71 38 485 1153 0 0 400 612 22 18 88 100 86 100 1596 1638 .52 1.923 2.377 2.493 1.847 2.376 52 319 1.822 .94 90 2040 8050 56 65 99 108 0 919 30 890 1.63 1007 977 .614 2.015 .705 1.011 .705
5 145 105 66 30 79 75 152 108 68 33 86 78 0 0 63 45 18 13 75 84 68 84 154 164 1.053 .949 .907 .995 .901 2.036 32 158 .804 .79 60 2220 8040 57 63 119 125 0 89 25 64 .805 92 66 1.243 .769 -.314 -.38 -.314
6 108 66 71 35 37 31 112 69 72 36 41 34 0 0 34 20 21 14 71 71 46 56 68 75 1.194 .838 .829 .623 .56 2.162 32 151 .536 .55 60 2330 8050 58 64 130 136 0 56 30 26 .71 58 29 1.408 .703 -.494 -.509 -.494
7 230 68 68 35 162 33 253 67 70 37 185 32 0 0 92 26 18 11 90 80 84 65 195 217 4.909 .204 .173 .236 .227 2.03 52 320 .196 .76 90 2490 8040 55 64 144 153 0 58 30 28 .173 57 27 5.793 .147 -2.534 -2.77 -2.534
8 1478 4272 68 36 1410 4236 1633 4438 71 43 1565 4402 0 0 818 2238 21 42 100 100 98 100 5646 5967 .333 3.004 2.813 3.246 2.889 1.856 80 356 3 .96 100 2640 8040 55 65 159 169 0 3620 31 3590 2.546 3761 3731 .393 2.384 1.348 1.253 1.348
9 166 217 68 37 98 180 156 165 70 38 88 128 0 0 73 136 17 11 88 98 80 96 278 216 .544 1.837 1.455 1.764 1.669 1.769 52 278 1.938 .87 80 2780 8040 56 64 174 182 0 184 31 153 1.557 140 108 .642 1.233 .638 .302 .638
10 94 59 70 36 24 23 92 55 71 37 22 19 0 0 34 25 17 12 51 61 34 42 47 41 1.043 .958 .864 .869 .776 4.88 52 244 .587 .52 80 2940 8030 55 63 190 198 -50 50 31 19 .812 47 16 1.231 .732 -.45 -.3
11 301 355 68 34 233 321 324 398 71 37 256 364 0 0 152 188 19 16 91 97 86 93 554 620 .726 1.378 1.422 1.43 1.342 1.902 80 472 1.354 .91 110 3070 8040 54 65 201 212 0 301 29 272 1.168 337 308 .857 1.205 .223 .269 .223
12 161 144 65 37 96 107 156 135 72 42 91 98 0 0 60 59 29 18 91 91 75 83 203 189 .897 1.115 1.077 1.083 1.219 1.64 12 92 1.035 .83 50 3260 8040 57 62 223 228 0 122 31 91 .945 114 83 1.059 .913 -.082 -.132 -.082
13 154 128 65 33 89 95 158 115 67 34 93 82 0 0 61 86 17 10 80 80 78 76 184 175 .937 1.067 .882 .897 1.125 2.922 52 249 1.225 .7 80 3370 8040 56 64 233 241 0 108 28 81 .905 97 69 1.105 .747 -.145 -.42 -.145
14 94 58 62 34 32 24 85 55 65 35 23 21 0 0 40 32 16 10 55 53 42 50 56 44 1.333 .75 .913 .56 .565 3.278 52 264 .655 .55 80 3530 8030 55 63 249 257 -50 49 29 20 .636 47 18 1.573 .774 -.37 -.654
15 943 1589 65 34 878 1555 1001 1655 68 35 936 1621 0 0 619 1013 17 10 92 100 91 100 2433 2557 .565 1.771 1.732 2.048 1.691 2.056 80 325 1.74 .97 100 3670 8040 55 65 262 272 0 1347 29 1318 1.501 1403 1374 .666 1.468 .586 .554 .586
16 325 316 69 32 256 284 359 359 76 36 290 327 0 0 136 132 46 27 92 98 84 92 540 617 .901 1.109 1.128 1.179 1.117 1.496 52 308 1.037 .92 90 3800 8030 54 63 275 284 0 268 27 241 .94 304 277 1.064 .956 -.089 -.066 -.089
17 109 81 67 37 42 44 111 76 71 40 44 39 0 0 41 24 21 13 66 100 50 75 86 83 .955 1.048 .886 .931 .748 2.037 12 104 .468 .45 50 3980 8030 56 61 295 300 0 69 31 37 .888 64 33 1.126 .751 -.172 -.413 -.172
18 108 55 66 33 42 22 108 55 69 36 42 22 0 0 35 19 20 26 71 32 50 7 64 64 1.909 .524 .524 .502 .521 2.43 52 279 1.051 .46 80 4120 8040 56 64 308 316 0 47 28 19 .444 47 19 2.253 .444 -1.172 -1.172 -1.172
19 226 289 65 32 161 257 228 301 69 34 163 269 0 0 100 147 19 23 88 96 85 93 418 432 .626 1.596 1.65 1.538 1.581 2.086 80 360 1.662 .86 100 4260 8030 54 64 321 331 0 245 27 218 1.353 255 228 .739 1.399 .436 .484 .436
20 105 60 64 34 41 26 109 63 68 35 45 29 0 0 38 22 16 10 76 71 71 59 67 74 1.577 .634 .644 .568 .587 2.294 52 258 .41 .52 80 4400 8040 56 64 336 344 0 51 29 22 .537 53 25 1.861 .546 -.896 -.873 -.896

Total number of rows: 43008

Table truncated, full table size 8546 Kbytes.




Supplementary data files not provided
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