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Sample GSM81280 Query DataSets for GSM81280
Status Public on Nov 01, 2005
Title 9411
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 9411 Total RNA
Organism Homo sapiens
Characteristics 9411 Total RNA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Kidney, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51689.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 GPL3023
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
1 148 102 95 71 53 31 145 94 97 82 50 23 0 0 43 46 23 44 73 32 57 9 84 73 1.71 .585 .46 .635 .671 3.378 52 291 4.071 .11 90 1310 5400 47 56 34 43 0 112 78 34 .64 103 25 1.563 .503 -.644 -.991
2 234 118 94 76 140 42 244 95 97 86 150 19 0 0 124 117 22 46 67 31 65 17 182 169 3.333 .3 .127 .401 .324 5.312 80 364 .314 .28 100 1420 5400 47 57 45 55 0 129 83 46 .328 104 21 3.047 .139 -1.607 -2.851
3 282 173 95 74 187 99 256 164 97 84 161 90 0 0 190 93 22 46 69 55 67 48 286 251 1.889 .529 .559 .616 .538 2.633 52 282 .452 .66 80 1580 5400 48 56 62 70 0 189 81 108 .579 179 98 1.726 .612 -.788 -.709
4 147 107 97 84 50 23 150 107 99 88 53 23 0 0 44 49 25 45 68 34 50 12 73 76 2.174 .46 .434 1.086 1.05 4.192 32 232 2.153 .18 70 1740 5380 46 53 78 85 0 117 92 25 .503 117 25 1.987 .475 -.991 -1.075
5 112 75 98 79 14 -4 110 64 99 83 12 -15 0 0 32 37 19 42 40 12 21 0 10 -3 null null null 1.7 1.2 3.949 32 194 7.8 .14 70 1890 5390 47 54 93 100 0 82 86 -4 null 70 -16 null null null null
6 123 96 98 76 25 20 117 83 100 82 19 7 0 0 41 55 22 42 46 26 25 13 45 26 1.25 .8 .368 1.536 1.352 5.602 52 280 4.601 .2 80 2010 5390 47 55 105 113 0 105 83 22 .875 91 8 1.142 .403 -.192 -1.311
7 121 100 92 72 29 28 103 94 96 81 11 22 0 0 47 49 22 43 37 31 31 12 57 33 1.036 .966 2 .924 .98 6.21 32 169 1.927 .28 70 2190 5400 48 55 123 130 0 109 79 31 1.056 103 24 .947 2.188 .079 1.13
8 120 88 96 74 24 14 104 78 97 82 8 4 0 0 44 49 25 42 38 25 23 11 38 12 1.714 .583 .5 1.096 1.303 4.731 52 269 2.396 .21 80 2290 5400 48 56 133 141 0 96 81 15 .638 85 4 1.567 .547 -.648 -.87
9 118 86 97 76 21 10 119 78 99 84 22 2 0 0 28 44 23 45 47 21 18 5 31 24 2.1 .476 .091 .762 .871 6.381 80 335 -1 -1 100 2470 5390 46 56 150 160 0 94 83 11 .521 85 2 1.919 .099 -.941 -3.33
10 99 88 95 76 4 12 97 81 96 87 2 5 0 0 20 47 23 48 16 16 0 7 16 7 .333 3 2.5 2.321 2.132 3.278 120 445 -1 -1 130 2610 5390 44 57 162 175 0 96 83 13 3.282 89 5 .305 2.735 1.715 1.452
11 259 151 96 78 163 73 270 138 97 87 174 60 0 0 88 73 24 47 90 56 87 33 236 234 2.233 .448 .345 .421 .488 2.75 80 288 .511 .52 100 2740 5390 46 56 177 187 0 165 85 80 .49 151 66 2.041 .377 -1.029 -1.406
12 1054 769 97 80 957 689 612 525 100 87 515 445 0 0 959 710 23 45 85 71 76 65 1646 960 1.389 .72 .864 .862 .75 2.23 120 512 .728 .97 130 2890 5390 44 57 190 203 0 841 88 754 .788 574 487 1.269 .945 -.344 -.081
13 99 128 100 80 -1 48 94 119 102 87 -6 39 0 0 25 77 23 42 18 47 6 18 47 33 null null null 1.957 1.895 4.686 80 307 .023 .05 100 3050 5390 46 56 208 218 0 140 88 53 null 130 43 null null null null
14 107 84 100 83 7 1 104 71 101 92 4 -12 0 0 23 50 23 47 24 16 6 5 8 -8 7 .143 null 2.162 2.077 3.522 120 390 14.258 .1 120 3190 5390 45 57 221 233 0 92 91 1 .156 78 -13 6.398 null -2.678 null
15 97 131 96 82 1 49 97 119 99 92 1 37 0 0 22 74 24 48 16 41 1 19 50 38 .02 49 37 2.247 2.6 4.494 120 370 -1 -1 120 3320 5390 45 57 234 246 0 143 90 54 53.611 130 40 .019 40.482 5.744 5.339
16 946 990 100 78 846 912 1242 1121 102 88 1142 1043 0 0 625 734 23 46 90 82 85 75 1758 2185 .928 1.078 .913 .974 1.098 2.159 120 433 1.123 .95 130 3470 5390 44 57 248 261 0 1083 85 998 1.179 1226 1141 .848 .999 .238 -.001
17 170 212 99 81 71 131 177 187 101 89 78 106 0 0 58 132 23 45 70 65 60 55 202 184 .542 1.845 1.359 1.968 1.853 2.77 80 329 2.737 .65 100 3610 5380 45 55 264 274 0 232 89 143 2.019 205 116 .495 1.487 1.013 .572
18 96 92 100 84 -4 8 92 85 102 92 -8 1 0 0 23 44 23 46 11 16 2 3 4 -7 null null null 1.604 1.737 4.465 80 335 47.89 .03 100 3780 5390 46 56 281 291 0 101 92 9 null 93 1 null null null null
19 371 152 99 89 272 63 407 141 102 95 308 52 0 0 188 89 24 48 87 51 81 30 335 360 4.317 .232 .169 .282 .303 3.377 80 356 .263 .52 110 3910 5390 45 56 293 304 0 166 97 69 .253 154 57 3.946 .185 -1.98 -2.437
20 278 198 99 82 179 116 291 185 101 91 192 103 0 0 132 105 23 47 83 68 71 52 295 295 1.543 .648 .536 .763 .747 3.088 120 421 .685 .66 120 4050 5390 45 57 307 319 0 217 90 127 .709 202 113 1.41 .587 -.496 -.769

Total number of rows: 41472

Table truncated, full table size 8467 Kbytes.




Supplementary data files not provided
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