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Sample GSM81261 Query DataSets for GSM81261
Status Public on Nov 01, 2005
Title 8709
Sample type RNA
 
Channel 1
Source name Stratagene Universal Human Reference RNA
Organism Homo sapiens
Characteristics Stratagene Universal Human Reference RNA
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name 8709 Total RNA
Organism Homo sapiens
Characteristics 8709 Total RNA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Kidney, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49613.gif; format: 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 Oct 31, 2005
Last update date Oct 21, 2011
Contact name Hongjuan Zhao
E-mail(s) [email protected]
Phone 650-498-4922
Fax 650-723-0765
Organization name Stanford University
Department Urology, Edwards Building R116
Street address 300 Pasteur Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL3031
Series (1)
GSE3538 Conventional renal cell carcinomas
Relations
Reanalyzed by GSE33093

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
1 164 73 99 65 65 8 164 65 105 76 65 0 0 0 60 45 51 43 57 15 30 7 73 65 8.125 .123 null .718 .676 4.952 52 256 -1 -1 80 1580 6660 54 62 30 38 0 74 66 8 .125 66 0 8.02 null -3.004 null
2 356 85 99 64 257 21 343 84 105 75 244 20 0 0 79 53 31 42 100 25 100 7 278 264 12.238 .082 .082 .147 .158 2.733 52 246 .022 .13 80 1740 6670 55 63 46 54 0 86 65 21 .083 85 20 12.08 .083 -3.595 -3.59
3 1194 728 98 64 1096 664 1207 728 101 72 1109 664 0 0 271 275 29 40 100 100 100 98 1760 1773 1.651 .606 .599 .563 .611 1.579 52 277 .581 .85 90 1880 6670 54 63 59 68 0 738 65 673 .614 738 673 1.629 .607 -.704 -.721
4 120 76 95 69 25 7 113 71 98 75 18 2 0 0 35 40 28 40 42 21 13 3 32 20 3.571 .28 .111 2.327 1.573 5.437 52 264 .22 .12 80 2020 6660 54 62 74 82 0 77 70 7 .284 72 2 3.525 .113 -1.818 -3.151
5 117 87 100 75 17 12 119 78 105 81 19 3 0 0 28 45 40 40 15 21 1 7 29 22 1.417 .706 .158 1.122 1.25 3.425 52 302 -1 -1 80 2170 6660 54 62 89 97 0 88 76 12 .715 79 3 1.398 .16 -.484 -2.644
6 231 70 99 69 132 1 220 62 101 81 121 -7 0 0 47 42 28 44 100 6 100 6 133 114 132 .008 null .193 .165 2.561 32 206 11.93 .07 70 2320 6660 54 61 104 111 0 71 70 1 .008 63 -7 130.296 null -7.026 null
7 137 104 96 69 41 35 141 93 99 80 45 24 0 0 33 53 30 45 63 34 21 9 76 69 1.171 .854 .533 1.245 1.127 3.048 52 287 -1 -1 80 2460 6660 54 62 118 126 0 105 70 35 .865 94 24 1.156 .54 -.21 -.888
8 252 127 99 75 153 52 235 114 101 81 136 39 0 0 76 65 28 40 100 44 90 26 205 175 2.942 .34 .287 .342 .331 3.88 52 241 .288 .25 80 2620 6670 55 63 134 142 0 129 76 53 .344 115 40 2.904 .291 -1.538 -1.783
9 208 140 97 76 111 64 204 130 100 82 107 54 0 0 45 68 28 45 97 56 90 32 175 161 1.734 .577 .505 .563 .72 2.735 80 341 .932 .33 100 2760 6660 53 63 147 157 0 142 77 65 .584 132 55 1.712 .511 -.776 -.968
10 134 70 99 74 35 -4 134 57 101 82 35 -17 0 0 31 42 25 46 61 13 30 3 31 18 null null null 1.172 1.307 5.271 52 234 .106 .08 80 2900 6650 53 61 162 170 0 71 75 -4 null 58 -17 null null null null
11 445 231 96 72 349 159 434 227 101 85 338 155 0 0 120 104 28 53 100 82 100 68 508 493 2.195 .456 .459 .401 .457 2.25 80 321 .422 .66 100 3050 6670 54 64 176 186 0 234 73 161 .462 230 157 2.167 .465 -1.115 -1.106
12 1758 3772 99 71 1659 3701 1677 3626 101 87 1578 3555 0 0 584 910 29 77 100 100 100 100 5360 5133 .448 2.231 2.253 2.317 2.339 1.393 80 346 2.167 .93 100 3200 6660 53 63 191 201 0 3821 72 3749 2.26 3673 3601 .442 2.282 1.176 1.19
13 119 116 100 80 19 36 114 102 102 86 14 22 0 0 30 62 28 43 28 38 15 23 55 36 .528 1.895 1.571 2.19 2.555 3.985 52 243 7.317 .16 80 3340 6650 53 61 206 214 0 118 81 36 1.92 103 22 .521 1.592 .941 .671
14 116 152 98 81 18 71 116 138 101 84 18 57 0 0 32 80 25 44 38 55 13 40 89 75 .254 3.944 3.167 2.218 1.628 3.652 52 264 55.762 .03 80 3480 6650 53 61 220 228 0 154 82 72 3.996 140 58 .25 3.208 1.999 1.682
15 117 154 98 73 19 81 117 140 101 81 19 67 0 0 32 84 29 43 26 61 9 42 100 86 .235 4.263 3.526 2.649 2.235 2.884 52 273 11.075 .18 80 3630 6650 53 61 235 243 0 156 74 82 4.319 142 68 .232 3.572 2.111 1.837
16 2184 1841 99 77 2085 1764 2143 1798 102 90 2044 1721 0 0 517 473 26 80 100 100 100 100 3849 3765 1.182 .846 .842 .842 .852 1.272 80 353 .82 .9 100 3780 6660 53 63 249 259 0 1865 78 1787 .857 1822 1744 1.167 .853 -.222 -.229
17 183 234 104 80 79 154 180 225 105 89 76 145 0 0 44 98 28 48 92 88 69 76 233 221 .513 1.949 1.908 1.866 1.979 2.464 52 268 2.71 .54 90 3930 6670 54 63 264 273 0 237 81 156 1.975 228 147 .506 1.933 .982 .951
18 119 125 98 80 21 45 112 124 100 87 14 44 0 0 32 58 27 45 42 48 11 23 66 58 .467 2.143 3.143 1.943 2.086 4.459 52 255 10.206 .13 80 4070 6650 53 61 279 287 0 127 81 46 2.171 126 45 .461 3.184 1.118 1.671
19 1046 352 98 72 948 280 1010 317 100 81 912 245 0 0 200 149 29 44 100 98 100 93 1228 1157 3.386 .295 .269 .26 .252 1.796 80 381 .268 .72 110 4220 6650 51 62 292 303 0 357 73 284 .299 321 248 3.342 .272 -1.741 -1.878
20 379 248 98 83 281 165 387 231 106 94 289 148 0 0 87 114 53 60 97 81 96 61 446 437 1.703 .587 .512 .499 .536 2.663 120 480 .695 .64 130 4370 6660 51 64 306 319 0 251 84 167 .595 234 150 1.681 .519 -.749 -.947

Total number of rows: 41472

Table truncated, full table size 8510 Kbytes.




Supplementary data files not provided
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