[BioC] expression profile

[James W. MacDonald]

Hi Anupam,

anupam sinha wrote:
> Dear list,
>                    I use the following code to process some cel files I have
> :
> 
>> dat<-ReadAffy()
>> dat_norm<-rma(dat)
> Background correcting
> Normalizing
> Calculating Expression
>> dat_norm_mat<-exprs(dat_norm)
>>
> write.table(dat_norm_mat,"GSE3185.txt",sep="\t",row.names=T,col.names=T,quote=F)
> 
> and I get the following output in the text file :
>                             GSM48598.CEL         GSM48599.CEL
> GSM48600.CEL       GSM48601.CEL          GSM48602.CEL
>  100_g_at            3.47028618802937    3.49106274273872
> 3.46940719815954    3.46836687956259    3.45079245249753
> .
> .
> .
> 
>  I have couple of questions.
> 
> 1) How do I add one more column to the text file which will give the gene
> symbol for each of  the probe-id ?

library(hgu95av2.db)
symbols <- unlist(mget(featureNames(dat_norm), hgu95av2SYMBOL, 
ifnotfound = NA))

out <- data.frame(symbols, dat_norm_mat)

write.table(out, <you know the rest>)

Best,

Jim


> 2)  Do the expression values get log2 transformed (after "rma" normalization
> is done  on the cel files or I have to perform it separately) ?
> 
> This is my sessionInfo():
> R version 2.10.0 (2009-10-26)
> i386-redhat-linux-gnu
> 
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] splines   tcltk     stats     graphics  grDevices datasets  utils
> [8] methods   base
> 
> other attached packages:
>  [1] WGCNA_0.89          Hmisc_3.8-0         survival_2.35-7
>  [4] qvalue_1.22.0       flashClust_1.00     dynamicTreeCut_1.21
>  [7] impute_1.22.0       hgu95av2cdf_2.5.0   affy_1.24.2
> [10] Biobase_2.6.1       limma_3.2.3         R.utils_1.4.0
> [13] R.oo_1.7.2          R.methodsS3_1.2.0
> 
> loaded via a namespace (and not attached):
> [1] affyio_1.14.0        cluster_1.12.1       grid_2.10.0
> [4] lattice_0.17-26      preprocessCore_1.8.0 tools_2.10.0
> 
> Thanks in advance for any suggestions.
> 
> Regards,
> 
> Anupam
> 
> 
> 

-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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