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Sample GSM39950 Query DataSets for GSM39950
Status Public on Feb 21, 2005
Title Lymph node 2096
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Lymph node 2096
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-05/28321.gif
 
Submission date Jan 26, 2005
Last update date Nov 22, 2005
Contact name Jonathan Pollack
E-mail(s) pollack1@stanford.edu
Phone 650-736-1987
Organization name Stanford University
Department Pathology
Lab Pollack Lab
Street address 269 Campus Drive, CCSR3245A
City Stanford
State/province CA
ZIP/Postal code 94305-5176
Country USA
 
Platform ID GPL1824
Series (1)
GSE2193 Normal_human_tissues

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 same as UNF_VALUE but with flagged values removed
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
UNF_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

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 UNF_VALUE
1 130 68 68 37 62 31 129 66 72 39 61 29 0 0 36 21 21 16 84 75 78 40 93 90 2 .5 .475 .469 .508 2.637 32 191 .453 .54 70 1620 8330 49 56 46 53 0 59 32 27 .435 57 25 2.3 .413 -1.202 -1.274 -1.202
2 131 51 69 34 62 17 132 54 71 35 63 20 0 0 32 15 19 13 93 63 76 30 79 83 3.647 .274 .317 .278 .294 2.95 80 378 .268 .48 100 1770 8330 48 58 60 70 0 44 30 15 .238 47 17 4.194 .276 -2.068 -1.857 -2.068
3 249 518 70 34 179 484 251 538 70 36 181 504 0 0 59 141 16 10 98 100 97 100 663 685 .37 2.704 2.785 2.78 2.623 1.387 80 361 2.757 .93 100 1920 8330 48 58 75 85 0 450 30 421 2.351 468 438 .425 2.421 1.233 1.276 1.233
4 665 560 69 35 596 525 735 564 72 36 666 529 0 0 336 324 16 10 98 100 94 100 1121 1195 1.135 .881 .794 .948 .879 1.999 52 310 .914 .96 90 2070 8330 48 57 90 99 0 487 30 457 .766 490 460 1.306 .691 -.385 -.534 -.385
5 118 269 72 36 46 233 126 237 76 46 54 201 0 0 47 163 23 43 62 90 53 78 279 255 .197 5.065 3.722 4.308 4.423 1.614 32 197 4.304 .8 70 2200 8330 49 56 104 111 0 234 31 203 4.405 206 175 .227 3.237 2.139 1.695 2.139
6 137 52 71 34 66 18 134 51 74 41 63 17 0 0 37 18 21 36 90 12 81 0 84 80 3.667 .273 .27 .26 .291 3.099 32 205 .19 .44 70 2350 8340 50 57 119 126 0 45 30 16 .237 44 15 4.217 .235 -2.076 -2.091 -2.076
7 126 3070 68 35 58 3035 124 3536 70 37 56 3501 0 0 35 1435 17 11 85 100 72 100 3093 3557 .019 52.328 62.518 46.812 44.205 1.445 80 370 54.499 .82 100 2500 8330 48 58 133 143 0 2670 30 2639 45.502 3075 3044 .022 54.363 5.508 5.765 5.508
8 809 2174 70 34 739 2140 889 2417 72 36 819 2383 0 0 338 967 18 21 100 100 100 100 2879 3202 .345 2.896 2.91 3 2.983 1.489 80 357 2.969 .97 100 2650 8330 48 58 148 158 0 1890 30 1861 2.518 2102 2072 .397 2.53 1.332 1.339 1.332
9 153 174 71 34 82 140 156 172 73 35 85 138 0 0 50 81 17 10 88 98 80 96 222 223 .586 1.707 1.624 1.612 1.709 1.896 52 274 1.851 .82 80 2800 8320 48 56 164 172 0 151 30 122 1.485 150 120 .674 1.412 .57 .497 .57
10 104 51 69 36 35 15 98 49 71 36 29 13 0 0 36 19 16 10 65 57 40 34 50 42 2.333 .429 .448 .449 .468 2.761 52 254 .305 .46 80 2950 8320 48 56 179 187 -50 44 31 13 .373 43 11 2.683 .39 -1.359 -1.424
11 284 224 72 36 212 188 287 228 74 37 215 192 0 0 81 82 18 10 98 100 98 100 400 407 1.128 .887 .893 .842 .83 1.529 80 395 .931 .88 110 3090 8330 47 58 191 202 0 195 31 163 .771 198 167 1.297 .777 -.375 -.365 -.375
12 129 76 74 37 55 39 127 77 77 39 53 40 0 0 41 26 23 13 87 78 53 68 94 93 1.41 .709 .755 .641 .771 2.029 32 205 .656 .72 70 3220 8330 49 56 206 213 0 66 32 34 .617 67 35 1.622 .656 -.698 -.608 -.698
13 147 110 72 38 75 72 150 102 75 39 78 64 0 0 53 49 20 13 84 90 78 78 147 142 1.042 .96 .821 .871 .837 1.98 52 279 .912 .76 80 3380 8330 49 57 222 230 0 96 33 63 .835 89 56 1.198 .713 -.261 -.487 -.261
14 129 54 72 34 57 20 126 52 74 37 54 18 0 0 47 24 18 12 73 57 67 40 77 72 2.85 .351 .333 .322 .352 3.119 52 255 .294 .51 80 3540 8320 48 56 238 246 -50 47 30 17 .305 45 16 3.278 .29 -1.787 -1.713
15 587 431 74 36 513 395 667 448 74 38 593 412 0 0 251 201 17 12 98 100 98 98 908 1005 1.299 .77 .695 .743 .762 1.549 52 277 .767 .95 90 3680 8330 48 57 251 260 0 375 31 343 .67 390 358 1.494 .604 -.579 -.727 -.579
16 208 148 75 38 133 110 223 152 77 39 148 114 0 0 78 51 17 12 88 94 86 90 243 262 1.209 .827 .77 .827 .816 1.63 52 259 .771 .89 80 3810 8330 49 57 265 273 0 129 33 96 .719 132 99 1.39 .67 -.476 -.578 -.476
17 109 45 73 36 36 9 110 41 75 37 37 5 0 0 36 16 19 12 69 30 44 13 45 42 4 .25 .135 .268 .308 2.749 52 294 .231 .41 80 3980 8320 48 56 282 290 -50 39 31 8 .217 36 4 4.6 .118 -3.089 -2.202
18 127 51 77 39 50 12 136 46 79 41 59 7 0 0 52 27 21 12 75 25 58 8 62 66 4.167 .24 .119 .218 .167 2.569 12 104 .17 .38 50 4120 8330 50 55 297 302 0 44 34 10 .209 40 6 4.792 .103 -2.261 -3.277 -2.261
19 190 158 75 35 115 123 199 164 76 37 124 129 0 0 65 66 19 10 86 96 85 90 238 253 .935 1.07 1.04 .987 1.06 1.762 80 520 1.033 .82 110 4270 8320 46 57 309 320 0 137 30 107 .93 143 112 1.075 .905 -.105 -.145 -.105
20 124 49 78 36 46 13 127 45 80 38 49 9 0 0 47 16 19 10 71 46 65 31 59 58 3.538 .283 .184 .283 .291 2.682 32 165 .159 .42 60 4430 8320 49 55 328 334 0 43 31 11 .246 39 8 4.069 .16 -2.025 -2.646 -2.025

Total number of rows: 43008

Table truncated, full table size 8630 Kbytes.




Supplementary data files not provided
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