[biomart-users] Strange results when changing gene labels

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[biomart-users] Strange results when changing gene labels

Richard Bownes
Hi,

I have never posted here before so I hope I format this question OK and supply sufficient information to get some answers.

I have been using biomart to replace gene ids for several months now, e.g. between ensembl_gene_ids and hgnc_symbols. I work in R and access biomart through the biomart package. Yesterday while trying to convert from hgnc symbols back to ensembl id my gene list was reduced from 15K to 300 genes. There is always a slight reduction, but this is catastrophic in terms of what I can use the data set for. Has any one encountered this behaviour before or has any experience with a problem like this? I believe the data I am working with is confidential in nature, so I don't know how much I could post for feedback. 

Best wishes,
Richard.  

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Re: [biomart-users] Strange results when changing gene labels

Thomas Maurel
Dear Richard,

Could you please send me the exact query that you are running in the biomaRt R package so that I can investigate?

Thanks a lot,
Kind Regards,
Thomas
On 30 Mar 2017, at 14:53, Richard Bownes <[hidden email]> wrote:

Hi,

I have never posted here before so I hope I format this question OK and supply sufficient information to get some answers.

I have been using biomart to replace gene ids for several months now, e.g. between ensembl_gene_ids and hgnc_symbols. I work in R and access biomart through the biomart package. Yesterday while trying to convert from hgnc symbols back to ensembl id my gene list was reduced from 15K to 300 genes. There is always a slight reduction, but this is catastrophic in terms of what I can use the data set for. Has any one encountered this behaviour before or has any experience with a problem like this? I believe the data I am working with is confidential in nature, so I don't know how much I could post for feedback. 

Best wishes,
Richard.  

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Thomas Maurel
Bioinformatician - Ensembl Production Team
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom

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Re: [biomart-users] Strange results when changing gene labels

Richard Bownes
Emailed them to you!


On Thursday, 30 March 2017 16:19:46 UTC+1, Thomas Maurel wrote:
Dear Richard,

Could you please send me the exact query that you are running in the biomaRt R package so that I can investigate?

Thanks a lot,
Kind Regards,
Thomas
On 30 Mar 2017, at 14:53, Richard Bownes <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="HLpZ5gfHCQAJ" rel="nofollow" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">rjbo...@...> wrote:

Hi,

I have never posted here before so I hope I format this question OK and supply sufficient information to get some answers.

I have been using biomart to replace gene ids for several months now, e.g. between ensembl_gene_ids and hgnc_symbols. I work in R and access biomart through the biomart package. Yesterday while trying to convert from hgnc symbols back to ensembl id my gene list was reduced from 15K to 300 genes. There is always a slight reduction, but this is catastrophic in terms of what I can use the data set for. Has any one encountered this behaviour before or has any experience with a problem like this? I believe the data I am working with is confidential in nature, so I don't know how much I could post for feedback. 

Best wishes,
Richard.  

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Thomas Maurel
Bioinformatician - Ensembl Production Team
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom

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Re: [biomart-users] Strange results when changing gene labels

Thomas Maurel
Thanks a lot Richard.
This is quite a large list of ensembl gene ids. Could you please try to split this list into smaller chunks of let say 500 ids?
You can then run the following code multiple time using 500 ids at a time:
ensembl <- useMart("ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl", host = "www.ensembl.org")
getBM(attributes = c(filters, attributes),
filters = filters,
values = ids,
mart = ensembl)
}
This should make sure that you get back all the HGNC ids mapped to the Ensembl gene ids.
Hope this helps,
Kind Regards,
Thomas
On 3 Apr 2017, at 15:46, Richard Bownes <[hidden email]> wrote:

Emailed them to you!


On Thursday, 30 March 2017 16:19:46 UTC+1, Thomas Maurel wrote:
Dear Richard,

Could you please send me the exact query that you are running in the biomaRt R package so that I can investigate?

Thanks a lot,
Kind Regards,
Thomas
On 30 Mar 2017, at 14:53, Richard Bownes <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="HLpZ5gfHCQAJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;" class="">rjbo...@...> wrote:

Hi,

I have never posted here before so I hope I format this question OK and supply sufficient information to get some answers.

I have been using biomart to replace gene ids for several months now, e.g. between ensembl_gene_ids and hgnc_symbols. I work in R and access biomart through the biomart package. Yesterday while trying to convert from hgnc symbols back to ensembl id my gene list was reduced from 15K to 300 genes. There is always a slight reduction, but this is catastrophic in terms of what I can use the data set for. Has any one encountered this behaviour before or has any experience with a problem like this? I believe the data I am working with is confidential in nature, so I don't know how much I could post for feedback. 

Best wishes,
Richard.  

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Thomas Maurel
Bioinformatician - Ensembl Production Team
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom


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Thomas Maurel
Bioinformatician - Ensembl Production Team
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom

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