Dear members,

I have methylation data for 4 tumor and 5 normal cases from Illumina 450k
array in iDAT format. I used methylumi package to read the idat files in R.
I am unable to get a way to export the probes with the intensity values and
corresponding genomic position (say TSS200, TSS1500 etc.). I want to see
the differences in methylation at different sites across tumor normal.
Please help. I use the following commands:

>
barcodes<-c("8963303122_R01C01","8963303122_R01C02","8963303122_R02C02","8963303122_R04C01","8963303122_R04C02","8963303122_R05C01","8963303122_R06C01","8963303142_R01C01","8963303142_R02C01","8963303142_R03C01")

> lumiset<-methylumIDAT(barcodes)
> normalized<-normalizeMethyLumiSet(lumiset)

>
write.table(file="normalized_beta_values.tsv",quote=F,sep="\t",data.frame(betas(normalized)))







sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C
 [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8
 [5] LC_MONETARY=en_US.utf8    LC_MESSAGES=en_US.utf8
 [7] LC_PAPER=C                LC_NAME=C
 [9] LC_ADDRESS=C              LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
 [1] IlluminaHumanMethylation450k.db_1.4.7 org.Hs.eg.db_2.8.0

 [3] RSQLite_0.11.2                        DBI_0.2-5

 [5] AnnotationDbi_1.20.3                  methylumi_2.4.0

 [7] ggplot2_0.9.3                         reshape2_1.2.2

 [9] scales_0.2.3                          Biobase_2.18.0

[11] BiocGenerics_0.4.0

loaded via a namespace (and not attached):
 [1] annotate_1.36.0    colorspace_1.2-1   dichromat_2.0-0    digest_0.6.3

 [5] genefilter_1.40.0  grid_2.15.0        gtable_0.1.2
IRanges_1.16.6
 [9] labeling_0.1       lattice_0.20-10    MASS_7.3-23        munsell_0.4

[13] parallel_2.15.0    plyr_1.8           proto_0.3-10
RColorBrewer_1.0-5
[17] splines_2.15.0     stats4_2.15.0      stringr_0.6.2
 survival_2.37-2
[21] tools_2.15.0       XML_3.95-0.1       xtable_1.7-1


Thanks in advance,
Srikanth


-- 
Srinivas Srikanth
Ph.D. Student
Institute of Bioinformatics
Discoverer, 7th Floor,
International Technology Park,
Bangalore, India
Mob:+919019114878, India

	[[alternative HTML version deleted]]

