Hi All I have a question regarding GEOqury package. I am using the following command. a) library(GEOquery) b) gse <- getGEO(filename="GSE21359_series_matrix.txt",GSEMatrix=TRUE). It works fine.And when i load the series matrix file then it downlaod the corresponding platform. soft file (e.g. GPL1319.soft in this case) from the internet,and save it in the tmp folder. This newly downloaded soft file by the GEOquery package is little bit different ( Hence not completely) from the GPL1319_family.soft file. Here my query is:- 1) "Can i upload these soft file before uploading series matrix so that instead of downloading the soft file from internet it will use the mention soft file?". If yes then HOW? 2) "In the above mention command b can i use the path of the soft file?". Again if yes then HOW?. REGARDS~ Reema Singh [[alternative HTML version deleted]]

On Mon, May 9, 2011 at 9:26 PM, Reema Singh <reema28sep@gmail.com> wrote: > Hi All > > I have a question regarding GEOqury package. I am using the following > command. > > a) library(GEOquery) > b) gse <- getGEO(filename="GSE21359_series_matrix.txt",GSEMatrix=TRUE). > > It works fine.And when i load the series matrix file then it downlaod the > corresponding platform. soft file (e.g. GPL1319.soft in this case) from the > internet,and save it in the tmp folder. > This newly downloaded soft file by the GEOquery package is little bit > different ( Hence not completely) from the GPL1319_family.soft file. Here > my > query is:- > > 1) "Can i upload these soft file before uploading series matrix so that > instead of downloading the soft file from internet it will use the mention > soft file?". If yes then HOW? > > Hi, Reema. You can specify a destdir in the getGEO command. All files will be downloaded to that directory. If there is a file of the appropriate name in that directory, the getGEO command will use that file before downloading. In other words, GEOquery tries to cache files in the destdir directory. If you were to replace the GPL file with one of the same name and it is a valid file, then GEOquery will pick that up instead of downloading. Just out of curiosity, where did the other soft file come from? I do not know of other software or vendors that are using the SOFT format. > 2) "In the above mention command b can i use the path of the soft file?". > Again if yes then HOW?. > > You cannot specify the path to the SOFT file directly. However, as I mentioned, you can save the file in the destdir directory and it should be used. Alternatively, you can always simply replace the featureData from the ExpressionSet with featureData of your choosing, including that obtained from a separate call to getGEO where you specify the path to the GPL file you have stored locally. Again, I'm not sure what the use case is here, so please clarify if what I describe is not what you need. Sean [[alternative HTML version deleted]]