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Lmfit function, to analyse differential expressions, not coming from arrays

Hi, i have to analyse the differential expression of 700 genes, for patients at diag and relapse i have normalized counts with log2 i would like the p value for each gene to perform a volcano plot and I wanted to use lmfit function from the limma package but is it possible without any probes? i have this message:

> E=read.table("nana.csv", header=TRUE, row.names=1,sep="\t", dec=".")
> A=as.matrix(E)
> F<-t(A)
> fit <- lmFit(F,design=NULL)
Error in getEAWP(object) : 
  **Data object doesn't contain numeric expression values**
gene
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updated by Devon Ryan Devon Ryan • written by claire.lamaison • claire.lamaison

Please follow the limma tutorial (i.e., use voom before lmFit rather than trying to transform things manually). Also, please have a look at A to help in diagnosing this.

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written by Devon Ryan Devon Ryan

hi Devon, thanks for your answer, 1- i received the data in log 2 2. because I have 10 patients I performed the arithmetic mean at diagnose, and at relapse, and I would perform the test but voom is for log transformation isn't it ? 3. what is A please? thanks claire

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written by claire.lamaison • claire.lamaison

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