Question: What is the criteria of logCPM? rpkm() error
0
gravatar for kanika.151
3.5 years ago by
kanika.15160
United States
kanika.15160 wrote:

Hello,

After getting results from edgeR, How do I know which logCPM values are significant and which are not?

I know that we can calculate RPKM values through edgeR by using

gdrpkm<- rpkm(data,gene.length=vector)

Error in gene.length/1000 : non-numeric argument to binary operator

 

myposts rna-seq edger • 1.5k views
ADD COMMENTlink modified 3.5 years ago by Devon Ryan90k • written 3.5 years ago by kanika.15160

Define "significant". logCPM values are logCPM values, there's no concept of significance typically attached to them.

ADD REPLYlink written 3.5 years ago by Devon Ryan90k

My RNA Seq data does not have technical replicates as the data was pooled into one. That is no replicates which won't give conclusive results per say which is why I cannot take P value or FDR values into consideration. I wanted to know if I had to deduce from logCPM values which genes are differentially expressed and which are not how would I do that? As in which is significant and which is not?

ADD REPLYlink written 3.5 years ago by kanika.15160
0
gravatar for Devon Ryan
3.5 years ago by
Devon Ryan90k
Freiburg, Germany
Devon Ryan90k wrote:

You can ignore the logCPMs, they're not useful for you. Pretty much the best you can do with your dataset is to use GFOLD.

ADD COMMENTlink written 3.5 years ago by Devon Ryan90k

Ohk. hmm. How reliable is GFOLD? Are there any publications made using that software?

ADD REPLYlink written 3.5 years ago by kanika.15160

For unreplicated data it's about as reliable as one can hope. You might be able to find publications using it, though if I were the reviewer I'd reject all studies lacking replicates (I'm not alone in this).
 

ADD REPLYlink written 3.5 years ago by Devon Ryan90k
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