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Sample GSM84884 Query DataSets for GSM84884
Status Public on Nov 23, 2005
Title s9797, p635, Pax
Sample type RNA
 
Channel 1
Source name Stratagene Universal Human Reference RNA, amplified from provided total RNA by AW 11/01
Organism Homo sapiens
Characteristics Stratagene Universal Human Reference RNA, amplified from provided total RNA by AW 11/01
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name s9797, p635, Pax
Organism Homo sapiens
Characteristics s9797, p635, Pax
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/25809.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 Nov 22, 2005
Last update date Sep 22, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) array@genome.stanford.edu
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 GPL3122
Series (1)
GSE3649 Individuality and variation in gene expression patterns in human blood.

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 3543 4058 316 157 3227 3901 3500 4112 323 169 3184 3955 0 0 593 723 73 92 100 100 100 100 7128 7139 .827 1.209 1.242 1.207 1.256 1.2 80 418 1.192 .97 100 2310 8920 24 34 30 40 0 3793 147 3646 1.13 3843 3696 .885 1.161 .176 .215
2 4232 8423 334 169 3898 8254 4264 8996 348 208 3930 8827 0 0 845 2031 98 246 100 100 100 100 12152 12757 .472 2.117 2.246 2.083 2.157 1.246 80 433 2.184 .98 110 2450 8910 22 33 43 54 0 7872 158 7714 1.979 8407 8250 .505 2.099 .985 1.07
3 3646 7615 333 173 3313 7442 3710 7757 349 221 3377 7584 0 0 657 1376 100 280 100 100 100 100 10755 10961 .445 2.246 2.246 2.252 2.288 1.208 80 449 2.306 .97 110 2620 8910 22 33 60 71 0 7117 162 6955 2.099 7250 7088 .476 2.099 1.07 1.07
4 4521 7558 314 168 4207 7390 4473 7875 324 192 4159 7707 0 0 683 1678 71 164 100 100 100 100 11597 11866 .569 1.757 1.853 1.725 1.858 1.292 80 401 1.813 .96 110 2770 8910 22 33 75 86 0 7064 157 6907 1.642 7360 7203 .609 1.732 .715 .792
5 3006 2226 317 167 2689 2059 2992 2226 331 182 2675 2059 0 0 806 651 85 93 100 100 100 100 4748 4734 1.306 .766 .77 .76 .76 1.188 80 421 .761 .97 110 2920 8910 22 33 90 101 0 2080 156 1924 .716 2080 1924 1.397 .719 -.483 -.475
6 3339 11525 328 172 3011 11353 3327 12164 334 197 2999 11992 0 0 615 2446 84 138 100 100 100 100 14364 14991 .265 3.771 3.999 3.741 4.014 1.272 80 422 3.959 .96 110 3090 8910 22 33 107 118 0 10771 161 10610 3.524 11368 11207 .284 3.737 1.817 1.902
7 5105 9813 339 185 4766 9628 5098 10562 348 209 4759 10377 0 0 1092 2626 78 139 100 100 100 100 14394 15136 .495 2.02 2.181 1.976 2.046 1.22 80 398 2.041 .97 110 3230 8920 23 34 121 132 0 9171 173 8998 1.888 9871 9698 .53 2.038 .917 1.027
8 3088 3088 340 185 2748 2903 3045 2992 344 195 2705 2807 0 0 637 732 78 81 100 100 100 100 5651 5512 .947 1.056 1.038 1.05 1.066 1.249 80 400 1.05 .96 100 3400 8910 23 33 139 149 0 2886 173 2713 .987 2796 2623 1.013 .97 -.018 -.044
9 2258 2630 315 169 1943 2461 2270 2572 324 186 1955 2403 0 0 405 442 80 85 100 100 100 100 4404 4358 .79 1.267 1.229 1.272 1.313 1.259 80 413 1.253 .94 110 3560 8910 22 33 154 165 0 2458 158 2300 1.184 2404 2246 .845 1.149 .243 .2
10 4261 6345 322 173 3939 6172 4317 6864 331 188 3995 6691 0 0 819 1586 80 84 100 100 100 100 10111 10686 .638 1.567 1.675 1.539 1.596 1.212 80 422 1.603 .98 110 3700 8910 22 33 168 179 0 5930 162 5768 1.464 6415 6253 .683 1.565 .55 .646
11 4668 5870 322 164 4346 5706 4366 5586 326 173 4044 5422 0 0 1077 1344 71 66 100 100 100 100 10052 9466 .762 1.313 1.341 1.315 1.327 1.155 80 372 1.287 .97 100 3860 8910 23 33 185 195 0 5486 153 5333 1.227 5221 5067 .815 1.253 .295 .325
12 3270 4517 308 159 2962 4358 3276 4807 312 174 2968 4648 0 0 585 1104 69 94 100 100 100 100 7320 7616 .68 1.471 1.566 1.436 1.537 1.274 80 425 1.515 .97 110 4010 8910 22 33 199 210 0 4221 149 4073 1.375 4493 4344 .727 1.464 .459 .55
13 3575 4584 310 168 3265 4416 3366 4516 313 181 3056 4348 0 0 841 1035 63 88 100 100 100 100 7681 7404 .739 1.353 1.423 1.354 1.393 1.217 80 400 1.334 .97 110 4170 8910 22 33 215 226 0 4284 157 4127 1.264 4221 4064 .791 1.33 .338 .411
14 11792 9728 321 184 11471 9544 13489 11419 330 191 13168 11235 0 0 4479 4700 73 67 100 100 100 100 21015 24403 1.202 .832 .853 .775 .841 1.305 120 428 .875 .98 120 4330 8920 23 35 231 243 0 9092 172 8920 .778 10672 10500 1.286 .797 -.363 -.327
15 5615 7378 301 165 5314 7213 5459 7526 309 173 5158 7361 0 0 1052 1615 65 66 100 100 100 100 12527 12519 .737 1.357 1.427 1.346 1.386 1.197 80 366 1.375 .98 110 4480 8910 22 33 246 257 0 6895 154 6741 1.269 7034 6879 .788 1.334 .343 .415
16 5953 18115 305 167 5648 17948 6724 20845 313 176 6419 20678 0 0 2246 7788 65 66 100 100 100 100 23596 27097 .315 3.178 3.221 3.145 3.229 1.23 120 427 3.298 .98 120 4640 8920 23 35 262 274 0 16930 156 16774 2.97 19481 19325 .337 3.011 1.57 1.59
17 8940 4992 310 162 8630 4830 8929 4752 317 176 8619 4590 0 0 1904 1474 79 85 100 100 100 100 13460 13209 1.787 .56 .533 .547 .545 1.188 80 373 .563 .98 110 4790 8910 22 33 277 288 0 4665 151 4514 .523 4441 4290 1.912 .498 -.935 -1.007
18 5633 4661 292 144 5341 4517 5518 4596 312 175 5226 4452 0 0 991 1003 166 200 100 100 100 100 9858 9678 1.182 .846 .852 .838 .832 1.141 80 474 .843 .99 110 4940 8900 21 32 292 303 0 4356 135 4221 .79 4295 4161 1.265 .796 -.339 -.329
19 2833 1453 301 151 2532 1302 2879 1590 324 176 2578 1439 0 0 1065 785 131 113 100 100 100 100 3834 4017 1.945 .514 .558 .442 .484 1.678 12 90 .553 .93 50 5110 8890 23 28 312 317 -100 1358 141 1217 .481 1486 1345 2.081 .522 -1.057 -.939
20 7631 4558 302 158 7329 4400 7655 4493 311 173 7353 4335 0 0 2039 1301 93 95 100 100 100 100 11729 11688 1.666 .6 .59 .597 .608 1.21 80 392 .599 .98 100 5260 8900 22 32 325 335 0 4260 148 4112 .561 4199 4051 1.782 .551 -.834 -.86

Total number of rows: 37632

Table truncated, full table size 8765 Kbytes.




Supplementary data files not provided
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