User: pixie@bioinfo

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pixie@bioinfo1.3k
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Posts by pixie@bioinfo

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Comment: C: Parallel computing while using R packages
... What appears that the program will be executed only if I give k=1 and takes almost 10-11 hrs for one network to be constructed. For every other value, it throws the above error. ...
written 4 weeks ago by pixie@bioinfo1.3k
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Comment: C: Parallel computing while using R packages
... Thank you, I will try this out. I am really stuck with this issue. ...
written 5 weeks ago by pixie@bioinfo1.3k
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Comment: C: Parallel computing while using R packages
... Hi Devon, I actually successfully constructed a gene correlation network of comparable size (actually slightly bigger) using the same package and the same server. However, this error I am getting after that. ...
written 5 weeks ago by pixie@bioinfo1.3k
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Parallel computing while using R packages
... A number of bioinformatic R packages allow us to specify the no. of threads (k) in the server. I am using the wTO package https://cran.r-project.org/web/packages/wTO/index.html used for construction of correlation networks which uses the library(parallel) for using multiple threads. I am running ...
R written 5 weeks ago by pixie@bioinfo1.3k • updated 5 weeks ago by Devon Ryan81k
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Comment: C: DESeq2- R commands for multiple groups
... Hi Devon, one last query. I am also interested in constructing co-expression networks with the rlog transformed data. `rlogged_data <- rlog(ds2)` How do I export rlogged_data object as a matrix (text or csv) for further analysis in WGCNA ? Thanks ...
written 5 months ago by pixie@bioinfo1.3k
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Comment: C: DESeq2- R commands for multiple groups
... Yes, I started with the DESeq2 paper, but the kept referring to the previous paper so had to read that one to get an idea. ...
written 5 months ago by pixie@bioinfo1.3k
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Comment: C: DESeq2- R commands for multiple groups
... Thanks a lot for the input ! ...
written 5 months ago by pixie@bioinfo1.3k
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Comment: C: RefSeq and mRNA
... You have any IDs or any disease/organism of interest ? You need to search based on that and the technology used. ...
written 5 months ago by pixie@bioinfo1.3k
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Comment: C: DESeq2- R commands for multiple groups
... Hi Devon, I was going through the DESeq (and DESeq2) papers to understand the models they are using, and also because I am a novice in this field. In the paper, they are calculating the size-factor which is explained here : http://seqanswers.com/forums/showpost.php?p=16468&postcount=13 So in my ...
written 5 months ago by pixie@bioinfo1.3k
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Comment: C: DESeq2- R commands for multiple groups
... Thanks for the pointers. I will try that out ...
written 5 months ago by pixie@bioinfo1.3k

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