User: m.azhar

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m.azhar0
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Posts by m.azhar

<prev • 13 results • page 1 of 2 • next >
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Network Export error and TOM object save error
... 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 reloa ...
rnaseq written 1 day ago by m.azhar0
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Comment: C: WGCNA error in network construction ?
... Thanks A lot for help Lluis but my Supervisor is not bioinformatic  so I have no help any I have move forward I used ssh 32 bit server to connect the linux based sever so I got TOM after 3.5 hours but i have two errors dim(TOM) 62103 62103  1. i wanted to save this data object but was not able to ...
written 1 day ago by m.azhar0
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Comment: C: WGCNA error in network construction ?
... yes that is final step names as  Exporting network data to network visualization software """ Exporting to VisANT The package provides a convenient function for exporting the network to VisANT [1]. We illustrate a simple export of the full weighted network of a single module. # Recalculate topologic ...
written 3 days ago by m.azhar0
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Comment: C: WGCNA error in network construction ?
... yes you right and thanks for input and advice, I already used block wise module approach for for network.Rdata file but for TOM=TOMsimilarityFromExpr(datExpr0, power =6); can i use bolck wise argument again ? or is there some other way to use network.Rdata file form blockwise module detection to c ...
written 3 days ago by m.azhar0
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Comment: C: WGCNA error in network construction ?
... how much time because yesterday I tried 4 times and after one hour at this step connection to server was disconnected, can I ask is this step is necessary to get export file or we can skip this  ...
written 3 days ago by m.azhar0
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network.Rdata file into TOM file error
... I am using WGCNA to build coexpression interaction network using lncRNA and mRNA consist of 62K probes so I used a sever which is command based with 64 GB RAM and blockwise module =8000 approach to calculate the modules and netwro.Rdata file. Now I want to export this network.Rata file to cytoscape ...
rnaseq written 3 days ago by m.azhar0
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Comment: C: WGCNA error in network construction ?
... I mean blockwise=2000 argument did not work , I used a server with 64 GB ram and have made network file but when I want to export the file I have to calculate The TOM according to WGCNA tutrioal but it TOM for data object gives no error but after some time it just do not go forward like  > TOM=T ...
written 3 days ago by m.azhar0
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Comment: C: WGCNA error in network construction ?
... yes you are right i read through these links before and again but i did not found any solution because I want to see lnc RNA and mRNA correlation network and one file contains more then 60 k probes i used block wise approach as suggested by WGCNA for 2000 but it did not work so what should i do guid ...
written 7 days ago by m.azhar0
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Comment: C: WGCNA error in network construction ?
... Dear Peter                       Thanks for advice yes you are right actually I am learning how to work in r. I used short code  like  data<-t(data) coexpression<-adjacency(data)  using  remote server now i want to convert save this file into .csv convert into cytoscape or visant file netw ...
written 8 days ago by m.azhar0
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Comment: C: WGCNA error in network construction ?
... I mean i used tutrioal object Expr but it has no data and i chekced bu str(Expr0) object Expr0 has the data so i used Expr0 object further in the script and data look  like  > str(Expr) Error in str(Expr) : object 'Expr' not found > str(datExpr0) 'data.frame':    18 obs. of  62103 variables: ...
written 8 days ago by m.azhar0

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