Adding information to the DESeq2 output file (gene name and expression levels for each sample(
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amyfm ▴ 10
@amyfm-9084
Last seen 5.8 years ago
Ireland

Hi,

 

After doing DESeq2 with RNA seq data, the output I obtain is an excel file with ensembl transcript ID, baseMean, log2FoldChange, lfcSE, stat, pvalue, and padj.

I would like to know 2 things:

-If you know if there is any code that I can use in order to obtain the gene name or description in the output file instead of the ensembl transcript ID

-If there is any code to obtain more columns in the output excel with the expression levels of each of my samples

 

Thank you


 

deseq2 gene columns output • 4.7k views
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@mikelove
Last seen 1 day ago
United States

See here:

http://www.bioconductor.org/help/workflows/rnaseqGene/#annotate

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The normalized counts for each sample can be obtained with

counts(dds, normalized=TRUE)

and you can add to the results table this with cbind ("column bind").

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thank you very much for your answer

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Hi,

I can't get the information I want (gene names on my excel output) as I get some error messages: Error in .testForValidKeys(x, keys, keytype, fks) : 
  None of the keys entered are valid keys for 'ENSEMBLTRANS'. Please use the keys method to see a listing of valid arguments.

 

I am using cows as a model, and my excel output is a columns with the ensembl transcripts IDs (appearing like this for example: transcript:ENSBTAT00000019061 

I would appreciate if someone give me the exact code for my case, as I am not very familiar with R and differential expression analysis but I need to have this information.

 

Thank you
 

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Annotation tasks like this typically take some amount of exploration/trial and error. If I came upon this error myself, I would compare the keys I was trying to use to query the database with the keys that are in the database, for example:

k <- keys(org.Xx.eg.db, keytype="ENSEMBLTRANS")
head(k)

Where Xx would be your organism. You can take a look at the AnnotationDbi vignette for more guidance.

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