Question: GOplot - tutorial
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gravatar for dimitrischat
11 months ago by
dimitrischat100
dimitrischat100 wrote:

Hi all, I am new in R and bioinformatics and i wanted to know what are the steps to prepare data for the R package - GOplot. I ve read the tutorial here : http://wencke.github.io/ , installed all packages needed. But i dont know how to prepare my data so i can import them into the R package and also from DAVID annotation online tool i dont know which annotation i should download. I got a .csv file with gene-ids (showing just 1 for example) from an rna-seq analysis (differential expression) looking like this :

> id    baseMean    baseMeanA   baseMeanB   foldChange  log2FoldChange  pval    padj
> CCL5  1922.0292307213 4.3818338728    3839.6766275698 876.2716111556  9.77523431  2.3E-58 1.34E-54

Any help would be appreciated.

rna-seq • 665 views
ADD COMMENTlink modified 11 months ago • written 11 months ago by dimitrischat100
0
gravatar for dimitrischat
11 months ago by
dimitrischat100
dimitrischat100 wrote:

From what i can see from EC$genelist it requires these columns

ID logFC AveExpr t P.Value adj.P.Val B

But i got

id baseMean baseMeanA baseMeanB foldChange log2FoldChange pval padj

What is AveExpr t and B compared to my data? (also i dont know what is "t" and "B")

obviously logFC = log2FoldChange P.Value = pval adj.P.Val = padj

Thanks

ADD COMMENTlink written 11 months ago by dimitrischat100
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