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Sample GSM69692 Query DataSets for GSM69692
Status Public on Aug 20, 2005
Title DT1 dye-swap MRC5
Sample type RNA
 
Channel 1
Source name cy3 DT1
Organism Homo sapiens
Characteristics desmoid tumor
Extracted molecule total RNA
Label cy3
 
Channel 2
Source name cy5 MRC5
Organism Homo sapiens
Characteristics primary fetal lung fibroblasts (MRC-5)
Extracted molecule total RNA
Label cy5
 
 
Description desmoid tumor from abdomen, patient with Gardner syndrome
Data processing print tip normalization without background substruction
 
Submission date Aug 12, 2005
Last update date Aug 15, 2005
Contact name Eugenia Migliavacca
Organization name ISREC
Lab BCF
Street address Ch des Boveresses 155
City Epalinges
State/province Vaud
ZIP/Postal code 1066
Country Switzerland
 
Platform ID GPL2746
Series (1)
GSE3127 Expression profiling of desmoid tumors and nodular fasciitis

Data table header descriptions
ID_REF
VALUE log2 ratio of intensities (CH1I)/(CH2I)
AVALUE average log2 total signal intensity
GRID subarray identifier
ROW row in the subarray
COL column in the subarray
CH1I uncorrected mean pixel intensity for channel 1 (Cy3)
CH1B median background pixel intensity for channel 1 (Cy3)
CH1AB mean background pixel intensity for channel 1 (Cy3)
CH2I uncorrected mean pixel intensity for channel 2 (Cy5)
CH2B median background pixel intensity for channel 2 (Cy5)
CH2AB mean background pixel intensity for channel 2 (Cy5)
SPIX number of pixels in a spot
BGPIX uniform background in the two channels
EDGE
RAT2
MRAT median of (Ch2PI-CH2B)/(Ch1PI-CH1B)
REGR slope estimate by simple linear regression
CORR correlation between channel1 and channel 2 pixels within the spot
LFRAT slope estimate by least-squares fit
CH1GTB1 fraction of pixels in the spot greater than background (CH1B)
CH2GTB1 fraction of pixels in the spot greater than background (CH2B)
CH1GTB2 fraction of pixels in the spot greater than 1.5 times the background (CH1B)
CH2GTB2 fraction of pixels in the spot greater than 1.5 times the background (CH2B)
CH1EDGEA mean magnitude of the horizontal and vertical Sobel edge vectors contained within each spot (CH1)
CH2EDGEA mean magnitude of the horizontal and vertical Sobel edge vectors contained within each spot (CH2)
FLAG user defined spot flag
CH1KSD value of the Komogorov-Smirnov statistic that assesses the likelihood that the spot pixel intensity distribution is drawn from the background distribution
CH1KSP actual probability derived from CH1KSD
CH2KSD value of the Komogorov-Smirnov statistic that assesses the likelihood that the spot pixel intensity distribution is drawn from the background distribution
CH2KSP actual probability derived from CH2KSD

Data table
ID_REF VALUE AVALUE GRID ROW COL CH1I CH1B CH1AB CH2I CH2B CH2AB SPIX BGPIX EDGE RAT2 MRAT REGR CORR LFRAT CH1GTB1 CH2GTB1 CH1GTB2 CH2GTB2 CH1EDGEA CH2EDGEA FLAG CH1KSD CH1KSP CH2KSD CH2KSP
1 null null 1 1 1 3127 71 120 18101 76 111 137 1419 0 5.898 5.515 5.224 0.9003 6.41 0.7518 0.9051 0.5839 0.7956 0.4501 0.5363 0 0.4741 2.181E-25 0.6242 1.079E-43
2 -0.0699 10.84 1 1 2 1514 71 126 2216 76 112 137 1353 0 1.483 1.411 1.143 0.8463 1.424 0.8832 0.9197 0.7445 0.8467 0.4209 0.4472 0 0.5879 1.191E-38 0.6985 0.000E+00
3 0.9215 11.67 1 1 3 1647 72 130 6483 76 107 137 1353 0 4.068 4.133 3.066 0.772 5.017 0.8905 0.8978 0.7664 0.8394 0.4344 0.5087 0 0.6332 9.809E-45 0.7068 0.000E+00
4 0.2394 8.07 1 1 4 222 72 129 326 77 113 137 1353 0 1.66 2.553 0.2482 0.2226 1.605 0.6861 0.7591 0.4234 0.5693 0.3367 0.3559 0 0.2664 2.837E-08 0.4064 1.095E-18
5 0.1306 7.76 1 1 5 183 73 127 255 77 113 137 1353 0 1.618 1.857 0.08879 0.09147 0.7266 0.5985 0.7518 0.3139 0.5839 0.3301 0.2971 0 0.1552 4.322E-03 0.3984 5.572E-18
6 1.904 10.92 1 1 6 803 73 153 4680 77 127 137 1348 0 6.305 6.838 3.929 0.6648 8.75 0.8467 0.8613 0.7445 0.8175 0.3965 0.4314 0 0.5334 7.040E-32 0.7361 0.000E+00
7 -4.7151 11.22 1 1 7 9512 74 280 596 77 133 137 1335 0 0.05499 0.04902 0.04129 0.6159 0.0414 1 0.9927 1 0.9343 0.2467 0.2601 0 0.9463 0.000E+00 0.7328 0.000E+00
8 -0.5643 9.8 1 1 8 1018 73 225 779 76 114 137 1353 0 0.7439 0.7768 0.3423 0.5683 0.4354 0.8905 0.8686 0.781 0.7518 0.3908 0.3333 0 0.5868 1.658E-38 0.587 1.574E-38
9 -2.9477 9.86 1 1 9 2436 71 119 356 76 110 137 1358 0 0.1184 0.118 0.07967 0.579 0.08068 0.8978 0.8467 0.8248 0.7007 0.4417 0.3464 0 0.6932 0.000E+00 0.5332 6.994E-32
10 2.2726 12.31 1 1 10 1543 72 123 16622 78 118 137 1363 0 11.25 11.76 8.238 0.8061 12.64 0.9197 0.9562 0.8467 0.9343 0.4146 0.4544 0 0.6982 0.000E+00 0.8671 0.000E+00
11 0.8486 12.4 1 1 11 2674 72 123 10971 77 119 137 1363 0 4.187 4.538 3.25 0.8669 4.252 0.927 0.9489 0.8686 0.9343 0.4462 0.4504 0 0.7384 0.000E+00 0.8539 0.000E+00
12 null null 1 1 12 1871 71 126 2586 76 116 137 1363 0 1.394 1.34 0.9667 0.7341 1.449 0.9051 0.9197 0.7883 0.8394 0.4901 0.5 0 0.6155 2.356E-42 0.6781 0.000E+00
13 1.6475 10.51 1 1 13 721 71 120 2953 76 112 137 1363 0 4.426 4.607 2.501 0.6803 5.197 0.927 0.9927 0.8102 0.9343 0.3755 0.4413 0 0.6377 1.401E-45 0.7875 0.000E+00
14 3.3419 12.01 1 1 14 871 71 116 19499 77 114 137 1363 0 24.28 26.42 15.96 0.7918 25.43 0.8905 0.9781 0.7664 0.9708 0.4103 0.4759 0 0.6058 4.857E-41 0.8948 0.000E+00
15 -3.2312 11.51 1 1 15 6468 72 124 1315 76 115 137 1363 0 0.1937 0.1874 0.1808 0.8748 0.1826 0.9343 0.9051 0.8978 0.8321 0.4631 0.4193 0 0.7786 0.000E+00 0.659 0.000E+00
16 -5.7497 11.2 1 1 16 13485 73 130 409 76 114 137 1363 0 0.02483 0.0242 0.02203 0.7206 0.02204 0.9708 0.8102 0.9343 0.6715 0.483 0.3465 0 0.8245 0.000E+00 0.5033 1.880E-28
17 -0.2988 11.57 1 1 17 2405 73 129 3855 76 112 137 1363 0 1.62 1.643 1.299 0.8916 1.522 0.9197 0.9562 0.8467 0.8905 0.429 0.4121 0 0.6675 0.000E+00 0.7983 0.000E+00
18 1.2081 11.95 1 1 18 1745 71 120 8933 77 118 137 1363 0 5.29 5.541 4.395 0.8706 5.745 0.9343 0.9781 0.8394 0.9489 0.414 0.4621 0 0.6827 0.000E+00 0.8516 0.000E+00
19 0.5892 12.24 1 1 19 2650 70 115 8814 76 117 137 1429 0 3.387 3.452 2.928 0.8986 3.566 0.9124 0.9562 0.8029 0.927 0.4911 0.5065 0 0.6651 0.000E+00 0.8232 0.000E+00
20 0.4745 12.32 1 2 1 2908 71 125 9043 75 109 137 1363 0 3.161 3.403 2.724 0.875 3.478 0.8467 0.9051 0.781 0.8394 0.4636 0.5271 0 0.6456 0.000E+00 0.7138 0.000E+00

Total number of rows: 11552

Table truncated, full table size 1889 Kbytes.




Supplementary data files not provided

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