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Sample GSM82119 Query DataSets for GSM82119
Status Public on Nov 05, 2005
Title wt TC2 T30
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/2000-07/7712.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 5110 5238 182 240 4928 4998 null null 562 429 null null null null null null null null 100 100 null null null null .986 1.014 null null .994 null 80 423 .989 .94 null null null 64 74 102 112 0 9883 452 9431 1.914 null null .523 null .936 null
2 6586 4098 218 229 6368 3869 null null 601 454 null null null null null null null null 100 100 null null null null 1.646 .608 null null .604 null 80 339 .577 .94 null null null 64 74 117 127 0 7732 432 7300 1.146 null null .872 null .197 null
3 3806 2622 195 215 3611 2407 null null 405 288 null null null null null null null null 98 93 null null null null 1.5 .667 null null .666 null 80 353 .668 .95 null null null 64 74 132 142 -100 4947 405 4542 1.258 null null .795 null .331 null
4 2182 677 383 265 1799 412 null null 654 326 null null null null null null null null 96 80 null null null null 4.367 .229 null null .217 null 52 246 .207 .75 null null null 64 72 148 156 -100 1277 500 777 .432 null null 2.315 null -1.211 null
5 6271 2259 752 310 5519 1949 null null 1553 545 null null null null null null null null 97 97 null null null null 2.832 .353 null null .383 null 80 356 .324 .92 null null null 63 73 162 172 -100 4262 584 3678 .666 null null 1.501 null -.585 null
6 6906 3526 193 241 6713 3285 null null 835 390 null null null null null null null null 100 100 null null null null 2.044 .489 null null .5 null 80 348 .48 .94 null null null 63 73 177 187 -100 6652 454 6198 .923 null null 1.083 null -.115 null
7 1553 1436 143 166 1410 1270 null null 166 183 null null null null null null null null 92 91 null null null null 1.11 .901 null null .924 null 80 364 .838 .93 null null null 63 73 192 202 0 2709 313 2396 1.699 null null .588 null .765 null
8 1561 1020 153 170 1408 850 null null 162 181 null null null null null null null null 100 94 null null null null 1.656 .604 null null .618 null 52 254 .582 .92 null null null 63 71 207 215 0 1924 320 1604 1.139 null null .878 null .188 null
9 16402 9465 160 175 16242 9290 null null 168 187 null null null null null null null null 100 100 null null null null 1.748 .572 null null .556 null 80 413 .528 .93 null null null 62 73 221 232 0 17858 330 17528 1.079 null null .927 null .11 null
10 1171 538 167 167 1004 371 null null 174 176 null null null null null null null null 98 88 null null null null 2.706 .37 null null .374 null 52 292 .398 .86 null null null 62 71 236 245 0 1015 315 700 .697 null null 1.434 null -.52 null
11 1617 482 150 169 1467 313 null null 172 213 null null null null null null null null 95 0 null null null null 4.687 .213 null null .225 null 80 364 .296 .32 null null null 62 72 252 262 0 909 318 591 .403 null null 2.482 null -1.312 null
12 7246 8492 147 170 7099 8322 null null 169 217 null null null null null null null null 100 98 null null null null .853 1.172 null null 1.153 null 80 347 1.072 .91 null null null 62 72 267 277 0 16022 320 15702 2.212 null null .452 null 1.145 null
13 4506 2479 148 168 4358 2311 null null 183 180 null null null null null null null null 100 98 null null null null 1.886 .53 null null .537 null 80 423 .547 .92 null null null 61 72 281 292 0 4677 316 4361 1.001 null null .999 null .001 null
14 18177 12226 183 203 17994 12023 null null 1683 927 null null null null null null null null 97 96 null null null null 1.497 .668 null null .664 null 80 347 .657 .95 null null null 62 72 297 307 -100 23067 383 22684 1.261 null null .793 null .334 null
15 6403 3754 190 212 6213 3542 null null 1619 978 null null null null null null null null 93 90 null null null null 1.754 .57 null null .582 null 80 338 .554 .85 null null null 62 72 311 321 -100 7083 400 6683 1.076 null null .93 null .105 null
16 3742 1867 155 171 3587 1696 null null 194 213 null null null null null null null null 100 96 null null null null 2.115 .473 null null .491 null 80 385 .491 .89 null null null 60 71 326 337 0 3522 322 3200 .892 null null 1.121 null -.165 null
17 9947 11170 164 183 9783 10987 null null 172 190 null null null null null null null null 100 100 null null null null .89 1.123 null null 1.116 null 120 484 1.102 .96 null null null 59 72 340 353 0 21075 345 20730 2.119 null null .472 null 1.083 null
18 172 179 172 183 null -4 null null 173 192 null null null null null null null null 12 12 null null null null null null null null .901 null 80 301 .062 .06 null null null 62 72 356 366 0 337 345 -8 null null null null null null null
19 7032 5028 161 181 6871 4847 null null 163 188 null null null null null null null null 100 96 null null null null 1.418 .705 null null .684 null 80 352 .699 .88 null null null 61 71 371 381 0 9486 341 9145 1.331 null null .751 null .412 null
20 2869 1775 155 187 2714 1588 null null 176 221 null null null null null null null null 94 86 null null null null 1.709 .585 null null .593 null 52 290 .574 .9 null null null 60 69 385 394 0 3349 352 2997 1.104 null null .906 null .143 null

Total number of rows: 24192

Table truncated, full table size 5828 Kbytes.




Supplementary data files not provided
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