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Sample GSM90054 Query DataSets for GSM90054
Status Public on Dec 30, 2005
Title PL116_4
Sample type RNA
 
Channel 1
Source name CRG
Organism Homo sapiens
Characteristics CRG
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name PL116_4
Organism Homo sapiens
Characteristics PL116_4
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Prostate, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32180.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 29, 2005
Last update date Sep 22, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) [email protected]
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 GPL3044
Series (1)
GSE3933 Prostate Cancer

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
1 257 77 91 62 166 15 250 79 98 65 159 17 0 0 87 24 40 22 93 34 81 12 181 176 11.067 .09 .107 .143 .148 2.4 32 212 .083 .37 70 1610 8220 46 53 65 72 0 104 84 20 .122 107 23 8.189 .144 -3.034 -2.791
2 316 89 86 55 230 34 313 84 93 58 227 29 0 0 123 32 35 21 92 63 90 38 264 256 6.765 .148 .128 .153 .163 2.291 52 324 .155 .6 90 1760 8220 45 54 79 88 0 120 74 46 .2 114 39 5.006 .173 -2.324 -2.534
3 1965 541 83 54 1882 487 1906 534 85 56 1823 480 0 0 815 265 23 16 100 100 97 97 2369 2303 3.864 .259 .263 .253 .267 1.746 80 437 .251 .93 110 1920 8220 44 55 94 105 0 731 73 658 .35 722 649 2.86 .356 -1.516 -1.491
4 3037 1388 83 53 2954 1335 3289 1473 86 54 3206 1420 0 0 1789 895 26 14 100 100 100 100 4289 4626 2.213 .452 .443 .416 .444 1.691 52 277 .448 .93 90 2060 8220 45 54 109 118 0 1876 72 1804 .611 1991 1919 1.637 .599 -.711 -.74
5 274 241 84 53 190 188 273 204 87 55 189 151 0 0 121 133 27 15 90 96 88 86 378 340 1.011 .989 .799 .92 .962 1.894 52 250 1.06 .87 80 2200 8220 46 54 124 132 0 326 72 254 1.337 276 204 .748 1.08 .419 .111
6 277 89 85 54 192 35 248 92 87 56 163 38 0 0 115 22 23 15 92 80 92 59 227 201 5.486 .182 .233 .199 .195 2.017 52 276 .135 .61 80 2360 8220 46 54 140 148 0 120 73 47 .246 124 51 4.059 .315 -2.021 -1.666
7 844 119 83 54 761 65 874 121 87 56 791 67 0 0 347 39 22 15 96 88 94 84 826 858 11.708 .085 .085 .085 .089 1.768 52 301 .077 .8 90 2500 8220 45 54 153 162 0 161 73 88 .115 164 91 8.664 .114 -3.115 -3.127
8 3662 1615 79 53 3583 1562 4013 1316 84 55 3934 1263 0 0 1812 1094 22 15 100 100 100 100 5145 5197 2.294 .436 .321 .413 .428 1.847 52 317 .447 .93 90 2650 8210 44 53 168 177 0 2182 72 2111 .589 1778 1707 1.697 .434 -.763 -1.205
9 698 338 80 57 618 281 640 290 84 58 560 233 0 0 458 255 24 16 96 98 90 92 899 793 2.199 .455 .416 .418 .421 2.065 52 315 .459 .87 90 2790 8220 45 54 182 191 0 457 77 380 .614 392 315 1.627 .562 -.703 -.831
10 163 74 85 56 78 18 161 67 91 64 76 11 0 0 42 26 48 54 78 12 34 0 96 87 4.333 .231 .145 .226 .204 2.577 32 164 .347 .38 60 2940 8210 46 52 199 205 0 100 76 24 .312 91 15 3.207 .196 -1.681 -2.354
11 1496 719 86 59 1410 660 1454 657 90 63 1368 598 0 0 711 311 32 33 100 100 99 99 2070 1966 2.136 .468 .437 .496 .472 1.587 120 541 .445 .95 120 3090 8210 43 55 211 223 0 972 80 892 .633 888 808 1.581 .591 -.661 -.759
12 422 191 93 63 329 128 367 169 94 67 274 106 0 0 261 96 26 24 96 96 93 84 457 380 2.57 .389 .387 .418 .431 2.276 32 181 .322 .78 70 3220 8210 45 52 226 233 0 258 85 173 .526 228 143 1.902 .523 -.928 -.936
13 431 388 84 58 347 330 380 370 88 60 296 312 0 0 241 242 22 18 96 98 94 94 677 608 1.052 .951 1.054 .868 .914 2.26 52 240 .974 .87 80 3370 8220 46 54 241 249 0 524 78 446 1.285 500 422 .778 1.424 .362 .51
14 206 86 84 60 122 26 198 85 86 61 114 25 0 0 67 22 20 18 90 65 90 21 148 139 4.692 .213 .219 .227 .227 1.556 32 218 .186 .58 70 3510 8210 45 52 255 262 0 116 81 35 .288 115 34 3.472 .296 -1.796 -1.755
15 2066 783 84 58 1982 725 2296 779 89 64 2212 721 0 0 1472 446 58 59 92 94 88 90 2707 2933 2.734 .366 .326 .489 .342 2.88 52 300 .317 .93 90 3660 8210 44 53 269 278 0 1058 78 980 .494 1053 974 2.023 .44 -1.017 -1.183
16 741 455 85 58 656 397 764 476 93 65 679 418 0 0 407 193 64 57 90 100 80 90 1053 1097 1.652 .605 .616 .776 .587 2.426 52 326 .529 .92 90 3800 8210 44 53 283 292 0 615 78 536 .818 643 565 1.223 .832 -.29 -.266
17 150 119 85 64 65 55 151 116 91 69 66 52 0 0 50 38 40 33 69 69 36 36 120 118 1.182 .846 .788 .709 .769 3.918 52 266 .952 .5 80 3950 8210 45 53 299 307 0 161 86 74 1.143 157 70 .875 1.065 .193 .09
18 191 72 85 61 106 11 196 67 87 64 111 6 0 0 42 26 23 35 96 9 93 3 117 117 9.636 .104 .054 .158 .17 2.436 32 200 .097 .25 70 4090 8210 45 52 313 320 0 97 82 15 .14 91 8 7.131 .073 -2.834 -3.775
19 893 742 85 61 808 681 933 787 97 72 848 726 0 0 372 261 65 59 100 100 100 98 1489 1574 1.186 .843 .856 .869 .772 1.603 80 433 .794 .91 100 4240 8210 44 54 327 337 0 1003 82 920 1.139 1064 981 .878 1.157 .188 .21
20 205 105 89 61 116 44 197 101 111 82 108 40 0 0 54 23 90 77 62 6 12 0 160 148 2.636 .379 .37 .381 .353 1.839 32 202 .362 .53 70 4390 8220 46 53 343 350 0 142 82 59 .513 136 54 1.951 .501 -.964 -.999

Total number of rows: 43008

Table truncated, full table size 8956 Kbytes.




Supplementary data files not provided
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