Thats great, thank you so much. There was a particular variable that had long strings that was being treated as a factor which caused the problems. It is now down to 13M without compression. That's more like it. Thanks Dan Adaikalavan Ramasamy wrote: > I am not an expert in R data representations. However, my experience > suggests that if an object is stored incorrectly as matrix instead of > data.frame, then the object sizes may be bloated. Also if it is a > data.frame, check that each column is stored correctly - via > matrix(obj). E.g. storing numeric columns as factors or characters etc. > > Also use the compress=TRUE option in the save(). > > Regards, Adai > > > > Daniel Brewer wrote: >> Hello, >> >> The GTF file from Ensembl for the human genome, >> Homo_sapiens.NCBI36.52.gtf, is 194M and is a tab-delimted text file. I >> import it into R and process it so that there are two objects: >> genomeRanges & genomeBlocks. genomeRanges is a list of IRanges objects, >> each of which is a particular chromosome and strand. genomeBlocks is a >> list of dataframes with the associated annotation for each of the >> transcripts. >> >> When I save this to file >> (save(genomeBlocks,genomeRanges,file="Hsgenome.Rdata")) it comes out as >> 859M. How is this possible? Especially as the Rdata file is a binary >> format. >> >>> object.size(genomeBlocks) >> [1] 2939935864 >> >>> object.size(genomeRanges) >> [1] 8769208 >> >> Anyway got any ideas what is going on? >> >> Thanks >> >> Dan >> >> > -- ************************************************************** Daniel Brewer, Ph.D. Institute of Cancer Research Molecular Carcinogenesis Email: daniel.brewer at icr.ac.uk ************************************************************** The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the a...{{dropped:2}}