Network Export error and TOM object save error
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m.azhar ▴ 10
@mazhar-12584
Last seen 7.5 years ago

HI 

I have tried a matrix of 62103 62103 dimension to calclulate TOM on ssh server 32 bit connection to linux baser server using R WGCNA package but It took 3.5 hours to calculate any how after that i wanted to save this object so that if the connection is disconneted or R is terminated i can reload it from R.data file but i feel this error

1. > save(TOM, file="mat1.rda", compress="xz")
Error in save(TOM, file = "mat1.rda", compress = "xz") : fwrite error
Error in close.connection(con) : fwrite error

 

2. I wanted to export this obejct as network file but i face this error 

vis=exportNetworkToVisANT(modTOM, file=paste( "VisANTInput-", module, ".txt", Warning messages:TRUE, threshold=0)
1: In max(abs(adjMat - t(adjMat)), na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf
2: In min(adjMat, na.rm = TRUE) :
  no non-missing arguments to min; returning Inf
3: In max(adjMat, na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf
4: In matrix(c(1:nRow), nRow, nRow, byrow = TRUE) :
  data length exceeds size of matrix
5: In matrix(c(1:nRow), nRow, nRow) : data length exceeds size of matrix

 

what is the better solution, Thanks for advice and suggestion in advance 

rnaseq • 929 views
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