Affymetrix microarray data analysis to do, choose which uniform method? Use Li-Wong model that can be corrected PM-MM; choose which tools to do it? With dChip.
Report of the first day after the end of the evening arrangements for students and Rapporteur held talks with me and Li bedroom early to come to the meeting, all the door, so that air conditioning role to play point, the effect is obvious, no further steam on the position of young people carrying a bag that is the day to do Genomic analysis of cancer genome using SNP microarrays Cheng Li, the report of the report, the report said the person he used to do these analysis dchip was very surprised to see this presentation, Why is a tool used specifically mention it, but I have always been done with dchip homogenization, and then export the data using other tools to do further analysis, can complete all of it?
chatted up, dchip that he developed a, Li-Wong model is his Li, Kuang Han!!! blame people do not report detailed the background, there is no concern about the use of good tools for developers, future attention.
back to catching it, found dchip can do genetic screening, time series analysis can be done, you can do enrichment analysis, chromosome mapping can do ......< br> The analysis I have overcome the difficulties of his own, to find a way, programming solution, originally such a good tool to have been resolved.
OH, MY GOD! kill a chicken with a chopper, chopper does not make good use of.
Fortunately, in the process of exploring a lot of things to learn.
Attachment: Tongji University of overseas experts in Bioinformatics Professional Profile
Name: Lee Cheng
Sex: Male Date of birth:
1975 年 1 月 department:
Institute of Life Science and Technology, Tongji University administrative functions
:
Degree: Instructor Dr.
situation:
doctoral research
:
bioinformatics, computational genomics, and neuroscience in the field of cancer and the application of
E-mail: < br> lch3000@gmail.com
Tel:
Address:
1239 Siping Road, Shanghai, Tongji University, College of Life Science and Technology (200092)
Introduction:
profile :
1995, graduated from Beijing Normal University, majoring in computer science, a bachelor's degree. In 2001 graduated from the University of California, Los Angeles, received Ph.D. in statistics. Since 2001, the Harvard School of Public Health and Dana-Farber Cancer Institute, Department of Biological Statistics and Computational Biology, a postdoctoral fellow research assistant professor in 2002, 2008, he was appointed Associate Professor. dChip software developed by the Study Group and associated data analysis methods are widely used in gene expression and SNP Biochip data analysis and presentation, the main articles cited more than 1,500 times. In Nature, Nature Genetics, Blood, PNAS, BMC Genomics and other publications published 60 papers. now as a PI project by the National Institutes of Health Research Grants R01.
Representative Articles (Selected Publications):
1. Li C, and Wong WH. Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection, Proc. Natl. Acad. Sci. 2001; 98, 31-36 < br> 2. Lin M, Wei LJ, Sellers WR, Lieberfarb M, Wong WH *, and Li C *. dChipSNP: Significance curve and clustering of SNP-array-based loss-of-heterozygosity data. Bioinformatics 2004; 20: 1233 -1240.
3. Zhao X, Li C, Paez JG, Chin K, Janne PA, Chen TH, Girard L, Minna J, Christiani D, Leo C, Gray JW, Sellers WR, Meyerson M. An integrated view of copy number and allelic alterations in the cancer genome using single nucleotide polymorphism arrays. Cancer Research 2004; 64:3060-3071.
4. Lu T, Pan Y, Kao SY, Li C,UGG shoes, Kohane I, Chan J, Yankner BA. Gene regulation and DNA damage in the ageing human brain. Nature 2004; 429:883 n891.
5. Leykin I, Hao K, Cheng J, Meyer N, Pollak MR, Smith RJH, Wong WH, Rosenow C *, Li C *. Comparative linkage analysis and visualization of high-density oligonucleotide SNP array data. BMC Genetics 2005; 6:7.
6. Garraway LA, Widlund HR, Rubin MA, Getz G, Berger AJ, Ramaswamy S, Beroukhim R, Milner DA, Granter SR, Du J, Lee C, Wagner SN,cheap UGG boots, Li C, Golub TR,UGG boots cheap, Rimm DL, Meyerson ML, Fisher DE,UGG boots, Sellers WR. Integrative genomic analyses identify MITF as a lineage survival oncogene amplified in malignant melanoma. Nature 2005. 436 (7047) :117-22.
7. Beroukhim R, Lin M, Park Y, Hao K, Zhao X, Garraway LA, Fox EA, Hochberg EP, Mellinghoff IK, Hofer MD, Descazeaud A, Rubin MA, Meyerson M, Wong WH, Sellers WR *, Li C *. Inferring Loss-of-Heterozygosity From Tumor-only Samples Using High-Density Oligonucleotide SNP Arrays. PLoS Computational Biology. 2006. 2 (5): e41. < br> 8. Johnson WE, Li C *, Rabinovic A. Adjusting batch effects in microarray expression data using Empirical Bayes methods. Biostatistics. 2007. 8 (1) :118-127.
9. Li C *, Beroukhim R , Weir BA, Winckler W, Garraway LA, Sellers WR, Meyerson M. Major copy proportion analysis of tumor samples using SNP arrays. BMC Bioinformatics. 2008. 9:204.
10. Li C. Automating dChip: toward reproducible sharing of microarray data analysis. BMC Bioinformatics. 2008. 9:231.
11. Li C, Kim SW, Rai D, Bolla AR, Adhvaryu S, Kinney MC, Robetorye RS, Aguiar RC. Copy number abnormalities, MYC activity and the genetic fingerprint of normal B-cells mechanistically define the microRNA profile of DLBCL. Blood. 2009. Published online.
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