Hello 
I am very thankful for the reply from Jim Holtman and David Winsemius, especially for the understandable explanations. it really works. 
Now I get another problem I cannot figure out. 
That is the situation: 
I work in biology. I need to download several files according to an experiment, which can be find out in NCBI GEO, and store them. 
For this I use GEOquery package and getGEO function. 
Each experiment (named GSE) contains several Samples (GSM), which names I extract by names(GSMList()). 
So now I want to make association between the defined names, which represents lowercases names of GSM, having them from names(GSMList()) as 
class(names(GSMList(gse))) 
[1] "character" 

I wrote something like this 
lapply=(i=1:length(names(GSMList(gse))), lgsms[i]=getGEO(names(GSMList(gse))[i])) 
but 
"Error: unexpected ',' " or anything else 
if I try to make it directly by associating a name from the list to correspondent GEO file I get this 
lgsms[1]=getGEO(names(GSMList(gse))[1]) #lgsms - list of lowercases names from names(GSMList()) 
File stored at: 
/tmp/RtmpgnMuHv/GSM296650.soft # so it downloaded the file but didn't make the association with the name so I cannot use it. 
Error in lgsms[1] = getGEO(names(GSMList(gse))[1]) : 
incompatible types (from S4 to character) in subassignment type fix 

Generally, working with GEOquery should be done very careful, as previously I also have some problems regarding the characteristics of data extracted from it and the way to convert them in an affordable way. It is a pity, that authors don't give more explanations on it. So I suppose it is also here. 

Kind regards 
Alex Levitchi 


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