[BioMart Users] Missing Illumina Probe Ids when using biomaRt

classic Classic list List threaded Threaded
3 messages Options
Reply | Threaded
Open this post in threaded view
|

[BioMart Users] Missing Illumina Probe Ids when using biomaRt

Reuben Thomas

Hello,

 I am trying to get information on a probes from the illumina_humanwg_6_v1 platform using the R interface with the biomaRt library. For some reason, some probes (around 1500) seem to no longer have any information on ensembl. 

 For example, "0004730161" is a probe with no information through this interface,

> getBM(attributes=c("illumina_humanwg_6_v1", "hgnc_symbol", "entrezgene"), filters="illumina_humanwg_6_v1", values=c("0004730161"), uniqueRows=TRUE, mart=ensembl)

[1] illumina_humanwg_6_v1 hgnc_symbol           entrezgene           

<0 rows> (or 0-length row.names)

 where as,  "0006980528" is a probe that has information

> getBM(attributes=c("illumina_humanwg_6_v1", "hgnc_symbol", "entrezgene"), filters="illumina_humanwg_6_v1", values=c("0006980528"), uniqueRows=TRUE, mart=ensembl)

  illumina_humanwg_6_v1 hgnc_symbol entrezgene

1               6980528      ATP10D      57205

 The BioMart web interface on the ensembl website however does provide information for both these probes.
 I am at a loss at trying to explain the missing probes from the biomaRt R interface. Any help would be greatly appreciated.
Thanks,
Reuben Thomas


_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users
Reply | Threaded
Open this post in threaded view
|

Re: [BioMart Users] Missing Illumina Probe Ids when using biomaRt

Arek Kasprzyk
Hi Reuben,
it seems that BioMart Central that R is using is out of sync with Ensembl site. BioMart Central is on Ensembl 63 and Ensembl is already on 64.

Junjun:
Please update the BioMart Central Server to 64 asap

cheers,
a



On Thu, Sep 22, 2011 at 8:42 PM, Reuben Thomas <[hidden email]> wrote:

Hello,

 I am trying to get information on a probes from the illumina_humanwg_6_v1 platform using the R interface with the biomaRt library. For some reason, some probes (around 1500) seem to no longer have any information on ensembl. 

 For example, "0004730161" is a probe with no information through this interface,

> getBM(attributes=c("illumina_humanwg_6_v1", "hgnc_symbol", "entrezgene"), filters="illumina_humanwg_6_v1", values=c("0004730161"), uniqueRows=TRUE, mart=ensembl)

[1] illumina_humanwg_6_v1 hgnc_symbol           entrezgene           

<0 rows> (or 0-length row.names)

 where as,  "0006980528" is a probe that has information

> getBM(attributes=c("illumina_humanwg_6_v1", "hgnc_symbol", "entrezgene"), filters="illumina_humanwg_6_v1", values=c("0006980528"), uniqueRows=TRUE, mart=ensembl)

  illumina_humanwg_6_v1 hgnc_symbol entrezgene

1               6980528      ATP10D      57205

 The BioMart web interface on the ensembl website however does provide information for both these probes.
 I am at a loss at trying to explain the missing probes from the biomaRt R interface. Any help would be greatly appreciated.
Thanks,
Reuben Thomas


_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users



_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users
Reply | Threaded
Open this post in threaded view
|

Re: [BioMart Users] Missing Illumina Probe Ids when using biomaRt

Junjun Zhang
Yes, we are in the process of preparing Ensembl 64.
Junjun
Sent from my BBerry

 
From: Arek Kasprzyk [mailto:[hidden email]]
Sent: Thursday, September 22, 2011 08:56 PM
To: Reuben Thomas <[hidden email]>
Cc: [hidden email] <[hidden email]>
Subject: Re: [BioMart Users] Missing Illumina Probe Ids when using biomaRt
 
Hi Reuben,
it seems that BioMart Central that R is using is out of sync with Ensembl site. BioMart Central is on Ensembl 63 and Ensembl is already on 64.

Junjun:
Please update the BioMart Central Server to 64 asap

cheers,
a



On Thu, Sep 22, 2011 at 8:42 PM, Reuben Thomas <[hidden email]> wrote:

Hello,

 I am trying to get information on a probes from the illumina_humanwg_6_v1 platform using the R interface with the biomaRt library. For some reason, some probes (around 1500) seem to no longer have any information on ensembl. 

 For example, "0004730161" is a probe with no information through this interface,

> getBM(attributes=c("illumina_humanwg_6_v1", "hgnc_symbol", "entrezgene"), filters="illumina_humanwg_6_v1", values=c("0004730161"), uniqueRows=TRUE, mart=ensembl)

[1] illumina_humanwg_6_v1 hgnc_symbol           entrezgene           

<0 rows> (or 0-length row.names)

 where as,  "0006980528" is a probe that has information

> getBM(attributes=c("illumina_humanwg_6_v1", "hgnc_symbol", "entrezgene"), filters="illumina_humanwg_6_v1", values=c("0006980528"), uniqueRows=TRUE, mart=ensembl)

  illumina_humanwg_6_v1 hgnc_symbol entrezgene

1               6980528      ATP10D      57205

 The BioMart web interface on the ensembl website however does provide information for both these probes.
 I am at a loss at trying to explain the missing probes from the biomaRt R interface. Any help would be greatly appreciated.
Thanks,
Reuben Thomas


_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users



_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users