Undersøgelse af ikke lineære sammenhænge mellem codon ...
Undersøgelse af ikke lineære sammenhænge mellem codon ... Undersøgelse af ikke lineære sammenhænge mellem codon ...
Kilder: [1] Sharp PM, Li WH: The codon adaptation index: a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res 1987, 15:1281- 1295 [2] Li, C. and Wong, W.H. (2001) _Genome Biology_ *2*, 1-11. [3] Li, C. and Wong, W.H. (2001) _Proc. Natl. Acad. Sci USA_ *98*, 31-36. [4] Rafael. A. Irizarry, Benjamin M. Bolstad, Francois Collin, Leslie M. Cope, Bridget Hobbs and Terence P. Speed (2003), Summaries of Affymetrix GeneChip probe level data Nucleic Acids Research 31(4):e15 [5] Bolstad, B.M., Irizarry R. A., Astrand M., and Speed, T.P. (2003), A Comparison of Normalization Methods for High Density Oligonucleotide Array Data Based on Bias and Variance. Bioinformatics 19(2):185-193 [6] Irizarry, RA, Hobbs, B, Collin, F, Beazer-Barclay, YD, Antonellis, KJ, Scherf, U, Speed, TP (2003) Exploration, Normalization, and Summaries of High Density Oligonucleotide Array Probe Level Data. Biostatistics .Vol. 4, Number 2: 249-264 [7] Christopher Workman, Lars Juhl Jensen, Hanne Jarmer, Randy Berka, Laurent Gautier, Henrik Bj{\o}rn Nielsen, Hans-Henrik Saxild, Claus Nielsen, S{\o}ren Brunak, and Steen Knudsen. A new non-linear normal- ization method for reducing variability in dna microarray experiments. Genome Biology, accepted, 2002 22
[8] Cheng Li and Wing Hung Wong, Model-based analysis of oligonucleotides arrays: model validation, design issues and standard error application. Genome Biology 2001, 2(8):research0032.1-0032.11 [9] ftp://ftp.ncbi.nih.gov/genomes/Fungi/Saccharomyces_cerevisiae [10] http://www.ncbi.nlm.nih.gov/geo/ [11] http://www.bioconductor.org/biocLite.R (ygs98) 23
- Page 1 and 2: Undersøgelse af ikke lineære samm
- Page 3 and 4: Indledning Protein kodes af RNA, de
- Page 5 and 6: Data For at lave CAI beregninger, s
- Page 7 and 8: Normalisering af data For at kunne
- Page 9 and 10: Geometrisk gennemsnit Herefter bere
- Page 11 and 12: Beregning af optimal CAI Der beregn
- Page 13 and 14: Resultater Li og Sharps CAI Herunde
- Page 15 and 16: Pearson korrelation for ikke logari
- Page 17 and 18: Dicodon CAI For at få et overblik
- Page 19 and 20: Diskussion Den optimale CAI forudsi
- Page 21: Konklusion Det er blevet undersøgt
- Page 25 and 26: Normalisering af data: Sc.data.qsp
- Page 27 and 28: Koble genudtryk med gennavne source
- Page 29 and 30: Til Optimal CAI beregning kun gener
- Page 31 and 32: Beregning af CAI wk=0 CAI.vector.10
- Page 33 and 34: Beregning af CAI wk=0 CAI.vector.24
- Page 35 and 36: Beregning af CAI wk=0 CAI.vector.25
- Page 37 and 38: For alle gener...De 100 højst udtr
- Page 39 and 40: For alle gener...For de 24 højst u
- Page 41 and 42: For alle gener...De 250 højst udtr
- Page 43 and 44: Sammenligning mellem Li og Sharps C
- Page 45 and 46: Sammensætning af gener i dicodons:
- Page 47: Sammenligning mellem dicodon CAI og
Kilder:<br />
[1] Sharp PM, Li WH: The <strong>codon</strong> adaptation index: a measure of directional synonymous<br />
<strong>codon</strong> usage bias, and its potential applications. Nucleic Acids Res 1987, 15:1281-<br />
1295<br />
[2] Li, C. and Wong, W.H. (2001) _Genome Biology_ *2*, 1-11.<br />
[3] Li, C. and Wong, W.H. (2001) _Proc. Natl. Acad. Sci USA_ *98*, 31-36.<br />
[4] R<strong>af</strong>ael. A. Irizarry, Benjamin M. Bolstad, Francois Collin, Leslie<br />
M. Cope, Bridget Hobbs and Terence P. Speed (2003), Summaries of<br />
Affymetrix GeneChip probe level data Nucleic Acids Research 31(4):e15<br />
[5] Bolstad, B.M., Irizarry R. A., Astrand M., and Speed, T.P. (2003),<br />
A Comparison of Normalization Methods for High Density<br />
Oligonucleotide Array Data Based on Bias and Variance.<br />
Bioinformatics 19(2):185-193<br />
[6] Irizarry, RA, Hobbs, B, Collin, F, Beazer-Barclay, YD, Antonellis,<br />
KJ, Scherf, U, Speed, TP (2003) Exploration, Normalization, and<br />
Summaries of High Density Oligonucleotide Array Probe Level Data.<br />
Biostatistics .Vol. 4, Number 2: 249-264<br />
[7] Christopher Workman, Lars Juhl Jensen, Hanne Jarmer, Randy Berka, Laurent<br />
Gautier, Henrik Bj{\o}rn Nielsen, Hans-Henrik Saxild, Claus Nielsen, S{\o}ren<br />
Brunak, and Steen Knudsen. A new non-linear normal- ization method for reducing<br />
variability in dna microarray experiments. Genome Biology, accepted, 2002<br />
22
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