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 ?
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



-- 
Graduate Student,
Center For DNA Fingerprinting And Diagnostics,
4-1-714 to 725/2, Tuljaguda complex
Mozamzahi Road, Nampally,
Hyderabad-500001

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