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Sample GSM82135 Query DataSets for GSM82135
Status Public on Nov 05, 2005
Title actA TC1 T480
Sample type RNA
 
Channel 1
Source name CRE reference pool
Organism Homo sapiens
Characteristics CRE reference pool
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name experimental sample
Organism Homo sapiens
Characteristics experimental sample
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Pathogen, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2000-07/8092.gif
Data processing VALUE is Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Nov 04, 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 GPL2948
Series (1)
GSE3567 Listeria infection of Caco-2 cells

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
VALUE 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
LOG_RAT2N_MEDIAN 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 VALUE LOG_RAT2N_MEDIAN
1 3411 2788 207 161 3204 2627 null null 236 169 null null null null null null null null 96 100 null null null null 1.22 .82 null null .832 null 32 204 .792 .92 null null null 83 90 101 108 0 4725 272 4453 1.39 null null .72 null .475 null
2 7665 6147 213 167 7452 5980 null null 222 173 null null null null null null null null 100 100 null null null null 1.246 .802 null null .844 null 80 402 .776 .9 null null null 80 91 114 125 0 10418 283 10135 1.36 null null .735 null .444 null
3 3947 4548 180 145 3767 4403 null null 193 153 null null null null null null null null 100 100 null null null null .856 1.169 null null 1.205 null 80 445 1.127 .93 null null null 80 91 129 140 0 7708 245 7463 1.981 null null .505 null .986 null
4 3344 1755 191 148 3153 1607 null null 204 152 null null null null null null null null 93 93 null null null null 1.962 .51 null null .45 null 32 204 .437 .85 null null null 82 89 147 154 0 2974 250 2724 .864 null null 1.157 null -.211 null
5 6662 12946 191 154 6471 12792 null null 195 157 null null null null null null null null 100 100 null null null null .506 1.977 null null 2.027 null 80 423 1.904 .94 null null null 81 92 159 170 0 21942 261 21681 3.35 null null .298 null 1.744 null
6 4618 2587 191 152 4427 2435 null null 196 153 null null null null null null null null 98 93 null null null null 1.818 .55 null null .558 null 80 352 .565 .94 null null null 82 92 175 185 0 4384 257 4127 .932 null null 1.073 null -.101 null
7 6821 4442 175 139 6646 4303 null null 178 142 null null null null null null null null 98 92 null null null null 1.545 .647 null null .636 null 80 367 .624 .93 null null null 82 92 190 200 0 7528 235 7293 1.097 null null .911 null .134 null
8 2802 2214 161 137 2641 2077 null null 164 140 null null null null null null null null 97 91 null null null null 1.272 .786 null null .719 null 80 365 .707 .89 null null null 82 92 205 215 0 3752 232 3520 1.333 null null .75 null .414 null
9 16788 7368 151 140 16637 7228 null null 157 143 null null null null null null null null 100 98 null null null null 2.302 .434 null null .455 null 80 360 .436 .92 null null null 83 93 220 230 0 12488 237 12251 .736 null null 1.358 null -.441 null
10 1404 652 143 137 1261 515 null null 149 140 null null null null null null null null 100 91 null null null null 2.449 .408 null null .382 null 80 370 .445 .92 null null null 83 93 236 246 0 1105 232 873 .692 null null 1.444 null -.531 null
11 1934 829 148 134 1786 695 null null 151 137 null null null null null null null null 93 87 null null null null 2.57 .389 null null .388 null 80 338 .401 .91 null null null 83 93 251 261 0 1405 227 1178 .66 null null 1.516 null -.6 null
12 6177 6464 147 136 6030 6328 null null 151 140 null null null null null null null null 96 100 null null null null .953 1.049 null null 1.076 null 80 345 .996 .93 null null null 84 94 266 276 0 10955 230 10725 1.779 null null .562 null .831 null
13 5753 3306 143 136 5610 3170 null null 146 138 null null null null null null null null 100 100 null null null null 1.77 .565 null null .569 null 80 366 .553 .94 null null null 83 94 281 292 0 5603 230 5373 .958 null null 1.044 null -.062 null
14 15176 10083 146 136 15030 9947 null null 165 143 null null null null null null null null 100 99 null null null null 1.511 .662 null null .678 null 156 641 .66 .95 null null null 80 94 294 308 0 17089 230 16859 1.122 null null .892 null .166 null
15 2028 1087 160 146 1868 941 null null 188 155 null null null null null null null null 98 95 null null null null 1.985 .504 null null .517 null 80 387 .506 .93 null null null 83 94 310 321 0 1842 247 1595 .854 null null 1.171 null -.228 null
16 4490 1775 160 150 4330 1625 null null 166 154 null null null null null null null null 97 93 null null null null 2.665 .375 null null .378 null 80 362 .374 .95 null null null 84 94 327 337 0 3008 254 2754 .636 null null 1.572 null -.653 null
17 12421 14132 156 151 12265 13981 null null 161 153 null null null null null null null null 100 100 null null null null .877 1.14 null null 1.162 null 80 380 1.145 .95 null null null 84 95 340 351 0 23952 255 23697 1.932 null null .518 null .95 null
18 226 190 159 152 67 38 null null 166 156 null null null null null null null null 53 28 null null null null 1.763 .567 null null .444 null 80 357 .371 .44 null null null 85 95 356 366 0 322 257 65 .97 null null 1.031 null -.044 null
19 8558 5938 157 147 8401 5791 null null 165 152 null null null null null null null null 100 100 null null null null 1.451 .689 null null .726 null 80 347 .687 .95 null null null 85 95 371 381 0 10064 249 9815 1.168 null null .856 null .224 null
20 2899 1967 164 152 2735 1815 null null 172 157 null null null null null null null null 100 100 null null null null 1.507 .664 null null .665 null 80 344 .62 .94 null null null 86 96 386 396 0 3333 257 3076 1.125 null null .889 null .17 null

Total number of rows: 24192

Table truncated, full table size 5772 Kbytes.




Supplementary data files not provided
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