Question: Meta-analysis of gene expression data by 'MetaDE'
2
gravatar for Agaz Hussain Wani
3.7 years ago by
India
Agaz Hussain Wani260 wrote:

I want to perform meta-analysis of gene expression data by using 'MetaDE'

MetaDE.pvalue(x,meta.method='minP')

Where x is a list of matrix containing p-values with corresponding genes.

My data looks like 

           P.value   P.value.1
1007_s_at 0.000218932 0.000218932
1053_at   0.017000453 0.017000453
117_at    0.066864977 0.066864977
121_at    0.000218932 0.000218932
1255_g_at 0.320830091 0.320830091
1294_at   0.001602361 0.001602361

 

For The above code it give 

Error in matrix(NA, nrow(x$p), nm) : non-numeric matrix extent

I am not sure what is going wrong. Help appreciated. Thanks

R meta-analysis metade • 1.4k views
ADD COMMENTlink modified 3.3 years ago by Cherif Ben Hamda150 • written 3.7 years ago by Agaz Hussain Wani260
Answer: Meta-analysis of gene expression data by 'MetaDE'
2
gravatar for Cherif Ben Hamda
3.3 years ago by
Tunisia
Cherif Ben Hamda150 wrote:

Sorry For the late reply    #(maybe my response will be useful for for someone else)

Your x have to be list object with components : 

- p :  list of p values for each dataset.

so add the line below : 

x<-list(p=x)  

and then 

MetaDE.pvalue(x,meta.method='minP')

Cheers 

 

ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by Cherif Ben Hamda150
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