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Sample GSM81249 Query DataSets for GSM81249
Status Public on Nov 01, 2005
Title 9123
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 9123 Total RNA
Organism Homo sapiens
Characteristics 9123 Total RNA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Kidney, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49320.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
1 158 99 98 92 60 7 154 83 108 102 56 -9 0 0 32 70 129 52 1 15 0 7 67 47 8.571 .117 null .563 .74 4.243 52 288 .284 .49 80 2600 5370 29 37 40 48 0 101 94 7 .119 84 -9 8.427 null -3.075 null
2 597 163 108 108 489 55 603 178 113 114 495 70 0 0 147 76 34 57 100 56 100 18 544 565 8.891 .112 .141 .15 .164 3.318 32 225 .09 .26 70 2760 5370 29 36 56 63 0 166 110 56 .114 181 71 8.741 .144 -3.128 -2.797
3 1861 1623 107 101 1754 1522 2027 1729 114 111 1920 1628 0 0 686 583 35 55 100 100 100 100 3276 3548 1.152 .868 .848 .867 .878 1.406 52 288 .856 .96 90 2910 5380 29 38 70 79 0 1651 103 1548 .883 1759 1656 1.133 .862 -.18 -.213
4 119 102 101 95 18 7 116 99 103 104 15 4 0 0 38 48 29 52 30 17 15 1 25 19 2.571 .389 .267 1.828 1.529 3.692 52 254 -1 -1 80 3040 5360 28 36 84 92 0 104 97 7 .396 101 4 2.528 .271 -1.338 -1.882
5 126 92 100 97 26 -5 123 92 102 107 23 -5 0 0 27 46 29 53 34 9 9 1 21 18 null null null .739 1 6.989 52 273 .074 .08 80 3190 5360 28 36 99 107 0 94 99 -5 null 94 -5 null null null null
6 164 105 99 102 65 3 156 105 102 111 57 3 0 0 56 49 28 54 71 9 50 3 68 60 21.667 .046 .053 .505 .511 4.603 52 264 .481 .04 80 3330 5360 28 36 113 121 0 107 104 3 .047 107 3 21.301 .054 -4.413 -4.223
7 136 122 100 103 36 19 118 111 104 114 18 8 0 0 50 53 28 55 46 21 34 7 55 26 1.895 .528 .444 1.461 1.273 3.741 52 291 10.697 .05 80 3480 5360 28 36 128 136 0 124 105 19 .537 113 8 1.863 .452 -.897 -1.145
8 236 257 104 110 132 147 235 237 108 116 131 127 0 0 63 110 29 53 92 78 86 61 279 258 .898 1.114 .969 .992 1.019 2.948 52 286 1.939 .5 90 3640 5370 28 37 143 152 0 261 112 150 1.133 241 129 .883 .986 .18 -.02
9 235 258 107 104 128 154 232 233 110 115 125 129 0 0 56 114 29 55 100 86 92 60 282 254 .831 1.203 1.032 1.101 .98 2.425 80 380 1.942 .47 110 3770 5370 27 38 155 166 0 262 106 157 1.224 237 131 .817 1.05 .291 .07
10 133 120 109 118 24 2 127 117 112 126 18 -1 0 0 32 46 30 58 40 11 11 3 26 17 12 .083 null 1.124 1.322 4.694 52 244 38.67 .03 80 3920 5360 28 36 172 180 0 122 120 2 .085 119 -1 11.797 null -3.56 null
11 490 438 107 114 383 324 482 432 111 124 375 318 0 0 88 120 29 56 100 98 100 97 707 693 1.182 .846 .848 .801 .848 1.708 80 332 .9 .78 100 4070 5370 28 38 186 196 0 446 116 330 .86 439 323 1.162 .863 -.217 -.213
12 2965 6945 105 116 2860 6829 3364 7609 108 128 3259 7493 0 0 1403 2801 28 62 99 100 99 100 9689 10752 .419 2.388 2.299 2.638 2.389 1.651 120 427 2.341 .96 120 4220 5370 27 39 200 212 0 7064 118 6946 2.429 7740 7622 .412 2.339 1.28 1.226
13 159 186 111 123 48 63 150 179 112 131 39 56 0 0 44 75 31 59 55 46 34 21 111 95 .762 1.313 1.436 1.448 1.55 3.878 52 226 8.108 .17 80 4350 5360 28 36 215 223 0 189 125 64 1.335 182 57 .749 1.461 .417 .547
14 146 166 111 125 35 41 139 146 113 134 28 21 0 0 39 90 30 61 48 32 19 19 76 49 .854 1.171 .75 1.766 1.934 3.999 52 264 6.598 .23 80 4500 5360 28 36 230 238 0 169 127 42 1.192 149 21 .839 .763 .253 -.39
15 156 223 111 139 45 84 150 201 117 151 39 62 0 0 33 102 36 77 53 42 19 17 129 101 .536 1.867 1.59 1.955 1.925 3.165 52 244 7.456 .26 80 4640 5360 28 36 244 252 0 227 141 85 1.899 204 63 .527 1.617 .925 .693
16 2832 3265 112 134 2720 3131 2991 3323 133 169 2879 3189 0 0 722 605 146 185 100 100 98 100 5851 6068 .869 1.151 1.108 1.203 1.123 1.429 80 405 1.122 .96 110 4790 5360 26 37 257 268 0 3321 136 3185 1.171 3380 3244 .854 1.127 .228 .172
17 288 937 114 137 174 800 280 928 138 176 166 791 0 0 69 240 143 182 62 100 6 97 974 957 .218 4.598 4.765 4.854 4.656 1.72 80 417 4.536 .76 110 4940 5370 27 38 272 283 0 953 139 814 4.677 944 805 .214 4.847 2.225 2.277
18 137 269 115 146 22 123 133 266 126 155 18 120 0 0 34 95 57 72 13 59 0 38 145 138 .179 5.591 6.667 3.49 3.765 4.333 52 261 14.019 .2 80 5080 5360 28 36 288 296 0 274 149 125 5.687 271 122 .176 6.781 2.508 2.762
19 1803 910 119 135 1684 775 1838 873 127 149 1719 738 0 0 369 273 54 73 100 100 100 100 2459 2457 2.173 .46 .429 .446 .439 1.481 80 408 .447 .88 110 5230 5360 26 37 301 312 0 926 137 788 .468 888 751 2.136 .437 -1.095 -1.195
20 1086 522 117 135 969 387 1099 505 125 147 982 370 0 0 166 151 51 75 100 100 100 93 1356 1352 2.504 .399 .377 .371 .408 1.584 80 327 .37 .81 100 5380 5370 28 38 317 327 0 531 137 394 .406 514 376 2.462 .383 -1.3 -1.384

Total number of rows: 41472

Table truncated, full table size 8866 Kbytes.




Supplementary data files not provided

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