Hi I am working on co-expression analysis of rice dataset with the help of wgcna and R but now I am at one point which is showing error as shown below : dissTOM = 1-TOMsimilarityFromExpr(datExpr, power = 8); Error: cannot allocate vector of size 2.8 Gb In addition: Warning messages: 1: In matrix(0, nGenes, nGenes) : Reached total allocation of 2550Mb: see help(memory.size) 2: In matrix(0, nGenes, nGenes) : Reached total allocation of 2550Mb: see help(memory.size) 3: In matrix(0, nGenes, nGenes) : Reached total allocation of 2550Mb: see help(memory.size) 4: In matrix(0, nGenes, nGenes) : Reached total allocation of 2550Mb: see help(memory.size) Help me to resolve this problem -- View this message in context: http://r.789695.n4.nabble.com/Error-during-working-with-wgcna-and-R-tp4635768.html Sent from the R help mailing list archive at Nabble.com.
On 08.07.2012 13:02, deeksha.malhan wrote:> Hi > I am working on co-expression analysis of rice dataset with the help of > wgcna and R but now I am at one point which is showing error as shown below > : > > > dissTOM = 1-TOMsimilarityFromExpr(datExpr, power = 8); > Error: cannot allocate vector of size 2.8 Gb > In addition: Warning messages: > 1: In matrix(0, nGenes, nGenes) : > Reached total allocation of 2550Mb: see help(memory.size) > 2: In matrix(0, nGenes, nGenes) : > Reached total allocation of 2550Mb: see help(memory.size) > 3: In matrix(0, nGenes, nGenes) : > Reached total allocation of 2550Mb: see help(memory.size) > 4: In matrix(0, nGenes, nGenes) : > Reached total allocation of 2550Mb: see help(memory.size)> > Help me to resolve this problemYour problem requires in the next step at least 2.8Gb more memory, but you already allocated 2.5Gb which is your maximum, obviously. We really cannot help you to reduce the problem size without knowing anything about it. Uwe Ligges> -- > View this message in context: http://r.789695.n4.nabble.com/Error-during-working-with-wgcna-and-R-tp4635768.html > Sent from the R help mailing list archive at Nabble.com. > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >
I am also working on co-expression analysis. It seems like there is no way to use TOMsimilarityFromExpr for large datasets. The option 'maxBlockSize' exists for module detection but not for TOMsimilarity? The only solution seems to reduce the dataset On Sunday, July 8, 2012 1:02:54 PM UTC+2, deeksha.malhan wrote:> > Hi > I am working on co-expression analysis of rice dataset with the help of > wgcna and R but now I am at one point which is showing error as shown > below > : > > > dissTOM = 1-TOMsimilarityFromExpr(datExpr, power = 8); > Error: cannot allocate vector of size 2.8 Gb > In addition: Warning messages: > 1: In matrix(0, nGenes, nGenes) : > Reached total allocation of 2550Mb: see help(memory.size) > 2: In matrix(0, nGenes, nGenes) : > Reached total allocation of 2550Mb: see help(memory.size) > 3: In matrix(0, nGenes, nGenes) : > Reached total allocation of 2550Mb: see help(memory.size) > 4: In matrix(0, nGenes, nGenes) : > Reached total allocation of 2550Mb: see help(memory.size) > > Help me to resolve this problem > > -- > View this message in context: > http://r.789695.n4.nabble.com/Error-during-working-with-wgcna-and-R-tp4635768.html > Sent from the R help mailing list archive at Nabble.com. > > ______________________________________________ > R-h... at r-project.org <javascript:> mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >