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Question: A good alternative for RDavidWebService ??
1
gravatar for alakatos
2.4 years ago by
alakatos80
United States
alakatos80 wrote:

Hello, 

Some of my significant DE gene lists obtained by "Limma" contain far more than 3,000 genes. I tried to use the RDavidWebService through  "BACA" or "clusterProfiler" to retrieve functional annotation (e.g. KEGG).  Unfortunately,  I received error messages due to the size of my genelists as indicated on Davis website : "A job with more than 3000 genes to generate gene or term cluster report will not be handled by DAVID due to resource limit" ). 

I  am wondering what R packages or web resources would be a good alternative for "RDavidWebService".

Your advice is highly appreciated.

Thank you,

Anita 

ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by alakatos80

Since you are already using clusterProfiler, you could use the package's `enrichGO` or `enrichKEGG` functions. Check section 3 and 4 of the vignette

ADD REPLYlink written 2.4 years ago by António Miguel de Jesus Domingues380
2
gravatar for Gordon Smyth
2.4 years ago by
Gordon Smyth32k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth32k wrote:

Do you have Entrez Gene IDs for your genes? If so, you can simply use the kegga() function in limma to do the KEGG functional analysis.

Suppose that 'fit' is your fitted model object and you are testing for the second coefficient. Then you can call kegga() from the fit object using something like:

k <- kegga(fit, coef=2, geneid="EntrezID", species="Hs")
topKEGG(k)

This assumes you have human data and that the Entrez Gene IDs are contained in fit$genes$EntrezID.

You will need the very latest version of limma for this to work, so make sure you are using R 3.2.0 or 3.2.1 and type biocLite("limma") at the R prompt. You will also need to install the KEGGREST package.

As an aside, given the very large number of DE genes, you might consider using the treat() method in limma to prune the list down a bit to those with strongest effects.

ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by Gordon Smyth32k
1
gravatar for Cristobal Fresno Rodríguez
2.4 years ago by
Argentina/Cordoba/Universidad Católica de Córdoba (CONICET)

Hi Anita,

Unfortunatelly, DAVID's webservice api has the 3000 genes limit and 200 jobs per day. So, if you really need DAVIS's results, you can upload the genes manually in the website page and download the results into a file. Then, you can import them using RDavidWebService and continue with your pipeline.

Regards,

Cristobal

PS: let me know if other functionality needs to be develop and I'll update the package.

ADD COMMENTlink written 2.4 years ago by Cristobal Fresno Rodríguez350
0
gravatar for alakatos
2.4 years ago by
alakatos80
United States
alakatos80 wrote:

Thank you for advice. I was concerned about the large number of genes.

I will try both functions (treat and kegga).

Thanks once again,

Anita 

 

ADD COMMENTlink written 2.4 years ago by alakatos80
0
gravatar for branislav misovic
2.4 years ago by
Netherlands, Leiden
branislav misovic120 wrote:

hi Alakatos  , just additional tip ... 
   Once you get the KEGG  P.value scores from limma or others ...  check the dynamics & visualising network  in the top X KEGG  pathways by  using  great libs:
1) http://www.bioconductor.org/packages/release/bioc/html/pathview.html


2) http://www.bioconductor.org/packages/release/bioc/html/KEGGprofile.html

For me one important property is that you can visualize all samples on 1 Pathway.

Best,
Branko
 

ADD COMMENTlink written 2.4 years ago by branislav misovic120
0
gravatar for alakatos
2.4 years ago by
alakatos80
United States
alakatos80 wrote:

Thank you for all the great suggestions and help!  

Anita 

ADD COMMENTlink written 2.4 years ago by alakatos80
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