Adding information to the DESeq2 output file (gene name and expression levels for each sample(

Question: Adding information to the DESeq2 output file (gene name and expression levels for each sample(

4.0 years ago by

amyfm • 0

Ireland

amyfm • 0 wrote:

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 • 3.5k views

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modified 4.0 years ago by Michael Love ♦ 26k • written 4.0 years ago by amyfm • 0

Answer: Adding information to the DESeq2 output file (gene name and expression levels fo

4.0 years ago by

Michael Love ♦ 26k

United States

Michael Love ♦ 26k wrote:

See here:

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

ADD COMMENT • link written 4.0 years ago by Michael Love ♦ 26k

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").

ADD REPLY • link written 4.0 years ago by Michael Love ♦ 26k

thank you very much for your answer

ADD REPLY • link modified 3.9 years ago • written 4.0 years ago by amyfm • 0

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

ADD REPLY • link written 3.9 years ago by amyfm • 0

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.

ADD REPLY • link written 3.9 years ago by Michael Love ♦ 26k

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