r - Microarray Limma package, in topTable function don't assign ID for probsets column -


i tried tutorial daniel swan ,it works well. i'm facing problem in toptable function of limma package.

the "toptable" function create "probeset list" probset list have not "id" header (other columns name sample name, probe list column have not name (id)).

at result, when runing: 

gene.symbols <- getsymbol(probeset.list$id, "hgu133plus2")

i'm getting following error

  error in .select(x, keys, columns, keytype = extraargs[["kt"]], jointype = jointype):        'keys' must character vector

toptable is:

               logfc  aveexpr        t      p.value    adj.p.val        b 204779_s_at 7.367790 4.171707 72.77347 3.284937e-15 8.969850e-11 20.25762 207016_s_at 6.936667 4.027733 57.39252 3.694641e-14 5.044293e-10 19.44987 209631_s_at 5.192949 4.003992 51.24892 1.170273e-13 1.065182e-09 18.96660

my expression set achieved simpleaffy (gcrma) package. i'm runing r 3.0.2 under windows 7 latest bioconductor packages, simpleaffy_2.38.0 , limma_3.18.13 , anotation files: hgu133plus2.db_2.10.1 ,hgu133plus2probe_2.13.0, hgu133plus2cdf_2.13.0

i thankful, if me.

the ids not stored id column, rownames of table. change line to:

gene.symbols <- getsymbol(rownames(probeset.list), "hgu133plus2")

if want there id column instead of using row names, can assign 1 with:

probeset.list$id = rownames(probeset.list)

according documentation of toptable function, id column exist if , if there duplicated gene names:

 if ‘fit’ had unique rownames, row.names of above  data.frame same in sorted order. otherwise, row.names  of data.frame indicate row number in ‘fit’. if ‘fit’ had  duplicated row names, these preserved in ‘id’ column  of data.frame, or in ‘id0’ if ‘genelist’ contained  ‘id’ column.

in other examples you've seen id used, there must have been duplicate gene names in input. makes sense because r typically doesn't having duplicated rownames (but has no problem having duplicate ids in column).


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