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how to use build.mim function and on what type of data?

how to solve the error of :"Error in cor(dataset, method = estimator, use = "complete.obs") : no complete element pairs" befor using build.mim function in minet package

r
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written by mona • mona

please check; your genes should place in columns and samples in rows.

I think you read your original file with row.names = 1

simply read your file

then

mim <- build.mim(your.data,estimator="spearman")
• 0 views • link
written by zizigolu zizigolu

the columns contain the genes and rows have the samples .and while reading my file I didn't use row.names=1

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written by mona • mona

I have been facing the same issue. Have you found any solution yet ? If so could you please share how you overcame this problem ?

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written by akhilpotdar4405 • akhilpotdar4405

In your original data generaly genes are in row and samples in columns, if so; read your file so

your.data=t(read.table("your.data.txt", header = T, sep = "\t",row.names = 1))

then 

library(minet)

and

mim <- build.mim(your.data,estimator="spearman")
• 0 views • link
written by zizigolu zizigolu

Thank you for your reply.

your.data=t(read.table(file.choose(), header = T, sep = "\t",row.names = 1)) mim <- build.mim(your.data,estimator="spearman") Error in cor(dataset, method = estimator, use = "complete.obs") : no complete element pairs

i have been getting this error. whenever the gene list goes above 1000 . I have come to believe that this function is limited to a certain input range. I however want your outlook on this situation so that i can take a different route in my analysis.

my gene microarray dataset has 3264 genes across 6 timepoints

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written by akhilpotdar4405 • akhilpotdar4405

Add use="complete.obs" to build.mim

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written by zizigolu zizigolu

mim <- build.mim(genematrix,use="complete.obs") #Build Mutual Information Matrix Error in build.mim(genematrix, use = "complete.obs") : unused argument (use = "complete.obs")

This is the output after adding the parameter

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written by akhilpotdar4405 • akhilpotdar4405

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