[BioC] aggregate_summarizing expression values over entrez gene ids

[Vanessa Vermeirssen]

Hi,

I have a dataframe containing RMA normalized and summarized expression 
values for affymetrix probesets, av.data.
I have looked up the Entrez gene ids for the probesets in the annotation 
package, entrezids.
Multiple probesets map of course to the same entrez id and I would like 
to combine these data into one row,
by averaging the expression values for the same entrez ids over the 
different experiments.
I tried the function "aggregate" to do this, but somehow it gives an 
error that the arguments are not of the same length, but they are...???
How can I solve this or is there any other way to do this?

See my code below...

av.data <- read.table("humanGPL570avdata.txt", row.names = 1, sep = 
"\t", header = T, na.strings = "NA", fill = T)
av.data[1:5,1:5]
          X1_Schwann_p1 X1_Schwann_p3 X2_accumbens X2_adipose
1007_s_at      9.281857      9.340795     9.151775   8.319741
1053_at        7.000684      6.867318     4.633061   5.101534
117_at         6.007608      6.124562     5.425565   5.692270
121_at         6.543294      6.728119     7.651856   7.692947
1255_g_at      3.077289      2.989938     4.622865   2.955812
          X2_adipose_omental
1007_s_at           7.909480
1053_at             4.509407
117_at              6.298798
121_at              7.598834
1255_g_at           3.040816

probes <- ls(hgu133plus2ENTREZID)
entrezids <- unlist(mget(probes,hgu133plus2ENTREZID))
newdata <- data.frame(entrezids,av.data)

sum <- aggregate(av.data,as.list(entrezids),mean)
Error in FUN(X[[1L]], ...) : arguments must have same length

 > length(as.list(entrezids))
[1] 54675
 > dim(av.data)
[1] 54675    69

sumdata <- aggregate(newdata,as.list(newdata$entrezids),mean)
Error in FUN(X[[1L]], ...) : arguments must have same length
 > length(as.list(newdata$entrezids))
[1] 54675
 > dim(newdata)
[1] 54675    70


Thank you so much!
Vanessa

-- 
==================================================================
Vanessa Vermeirssen, PhD

Tel:+32 (0)9 331 38 10                       fax:+32 (0)9 3313809
VIB Department of Plant Systems Biology, Ghent University
Technologiepark 927, 9052 Gent, BELGIUM
vamei at psb.ugent.be                         http://www.psb.ugent.be