Dear All members,

I have been extracting data from GEO (GEO package) and do some analysis on them by using limma package. What I discover is the components of topTable(fit) are different from the dataset GDS and GSE.

If the data is from GDS, then the colnames of topTable (fit) looks like this.

> colnames(topTable(fit))
[1] "ID"                    "Gene.title"            "Gene.symbol"
 [4] "Gene.ID"               "UniGene.title"         "UniGene.symbol"
 [7] "UniGene.ID"            "Nucleotide.Title"      "GI"
[10] "GenBank.Accession"     "Platform_CLONEID"      "Platform_ORF"
[13] "Platform_SPOTID"       "Chromosome.location"   "Chromosome.annotation"
[16] "GO.Function"           "GO.Process"            "GO.Component"
[19] "GO.Function.1"         "GO.Process.1"          "GO.Component.1"
[22] "CTRL"                  "HIF1a"                 "HIF2a"
[25] "HIF1a2a"               "AveExpr"               "F"
[28] "P.Value"               "adj.P.Val"

If the data is from GSE, then the   colnames of topTable(fit) looks like this:

>colnames(topTable(fit)

[1] "ID"        "mir210"    "CTRL2"     "AveExpr"   "F"         "P.Value"   "adj.P.Val"

I am trying to add some term into this table by doing following one by one: the data is generated by Affymetrix human U133 platform:

>Library(hgu133plus2.db)
>x=hgu133plus2SYMBOL
>y=topTable(fit)
>y$SYMBOL=unlist(as.list(x[y$ID]))

It works but I need to add ENTREZID,SYMBOL,CHR, CHRloc, and GO annotations as well.  I like to have the topTable more like the topTable(fit) generated at top by data GEO GDS data

I am wondering if there is an easy way to annotate all once.

In addition, I am having a trouble to annotate GO term.

Many Thanks

Jing




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