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Question: Adding information to the DESeq2 output file (gene name and expression levels for each sample(
0
gravatar for amyfm
17 months ago by
amyfm0
Ireland
amyfm0 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


 

ADD COMMENTlink modified 17 months ago by Michael Love11k • written 17 months ago by amyfm0
0
gravatar for Michael Love
17 months ago by
Michael Love11k
United States
Michael Love11k wrote:

See here:

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

ADD COMMENTlink written 17 months ago by Michael Love11k

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 REPLYlink written 17 months ago by Michael Love11k

thank you very much for your answer

ADD REPLYlink modified 16 months ago • written 17 months ago by amyfm0

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 REPLYlink written 16 months ago by amyfm0

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 REPLYlink written 16 months ago by Michael Love11k
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