2) necessary package:
Biobase,
GEOquery
3) load the GPL platform file:
gpl5425 = getGEO('GPL5425',destdir=".")
## get annotation table
gpl5425_ann = Table(gpl5425)
#make the rownames to be ID
rownames(gpl5425_ann) = gpl5425_ann$ID
--------------------------------------------------------------------------------
ID GB_ACC GENE_SYMBOL
AA799301_PROBE1 AA799301_PROBE1 AA799301 LOC498225
AA799313_PROBE1 AA799313_PROBE1 AA799313 Siat10 ST3
AA799329_PROBE1 AA799329_PROBE1 AA799329 Col10a1
AA799331_PROBE1 AA799331_PROBE1 NM_001007634 Pelo
--------------------------------------------------------------------------------
#assume the expression data is:
gse24417
--------------------------------------------------------------------------------
ID_REF GSM204540 GSM204503 GSM204587 GSM204994
1 NM_016986_Probe1 14.5383 15.6827 14.0196 15.0969
2 NM_016987_Probe1 12.7629 15.6014 13.1481 14.4640
3 NM_016988_Probe1 14.0954 14.0583 13.6035 14.3924
4 M27893_Probe1 12.4787 12.6605 11.6335 14.0050
5 NM_012490_Probe1 8.9914 8.2654 9.2640 6.5239
--------------------------------------------------------------------------------
rownames(gse24417) = gse24417$ID_REF
#get the probe id, with upper character
pid = toupper(gse24417$ID_REF)
#get the gene symbol id
gid = gpl5425_ann[pid,]$GENE_SYMBOL
## gid contains empty value: "" , and NA value "NA", find the index of them and delete the lines.
blank_id = which( gid == "")
na_id = which(is.na(gid))
#now combine the final data
unwanted_index = c(blank_id,na_id)
gid = gid[-unwanted_index]
gse24417 = gse24417[-unwanted_index]
gse24417$ID_REF = gid
## now remove the repeated genes
