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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