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2.8 years ago
Morris_Chair ▴ 330
I used different tools to convert human gene ensemble ID to ENTREZ but each of them seems to have problems like: -BioMart does not recognizes all the ensemble ID but barely 30% , -BioDBnet ...I couldn't make it working cause I could only select the type of output , -DAVID gives me lots of false duplicates.
What do you usually use for this work ?
I use biomaRt (for ensembl to uniprot id conversion) and this works fine for me (not 100%, I still loose some ids, but this number is small). Maybe you could try to play around a bit with the "attributes" and "filters"?
Please show code and data examples. This is highly unlikely if used properly since biomart directly connects to Ensembl.
Hi ATpoint , here is the code
Probably there is something wrong with my hosting service?
Provide examples of identifiers that don't seem to map. It would also help to know where these ID's came from.
Thank you genomax, indeed.. most of them are non-coding RNA :)
BioMart, as others have mentioned, tends to work pretty well. Have you removed the version numbers off the end of the ensembl ID? (ie 1234567.89 --> 1234567)
Hi aaragak1, yes I did,
yes I did that, thanks :)
Are the ensembl IDs that you are working with derived from the current ensembl release?
Hi russh, yes they are thx, problem solved anyways. Most of those ensemble where from non coding RNA
Hi Arup Ghosh
Thanks for this code? Is the line Data$entrez calling the in which you want to convert the ENSEMBL Id's? and if so what is row.names(data) referring to - is it saying that the values are the rows in that file data. Should would specify the column in that brackets - such as (data$column).
I am trying to refer to a csv file that I have some ENSEMBL Id's in and I wish to convert these to ENTREZ id's as a new column. I was trying to use the packages above but I get
When I use this code:
ADD COMMENTto keep things logically organized.
keysargument is there to specify the column containing the Ensembl ids.
This will add a new(ENTREZID_id) column in your dataframe containing the Entrez ids.