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wgcna analysis on cel files

can any one help, how to load affymatrix cel files of control and treated into WGCNA package

rna-seq
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written by rajasekargutha • rajasekargutha

the thred you gave is very useful and i followed that code, but i coudnt annotate my data for gene symbols and entrez Ids though I've followed the steps to retrieve gene symbols. i am working on zebrafish cel files and i downloaded zebrafish.db package to get entrez id, but i am not getting ids and symbols.

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written by rajasekargutha • rajasekargutha

2 answers

You should be using the standard way of processing the .cel files and use the normalized expression data as input to WGCNA. Take a look at this thread and read carefully all the threads. WCGNA accepts the expression data as input so the normalized expression matrix should work

In any case what I meant to say is use any procedure or any tool like limma (not endorsing but the most widely used one) or other tools to process and normalize(any normalizer which best fits to your data) your cel files and then create an expression matrix which should be used as an input for WGCNA package.

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written by ivivek_ngs ivivek_ngs

Please accept or validate the answer if it is of use so that others can use it for future reference.

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written by ivivek_ngs ivivek_ngs

How to create trait file for control and stress samples for Wgcna analysis

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written by rajasekargutha • rajasekargutha

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