[BioMart Users] biomaRt query

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

[BioMart Users] biomaRt query

Natasha Sahgal
Hello,

I am new to using biomaRt, and I use it via the R/Bioconductor package.

However, there are some things I do not understand.

1) What is the difference between: "with_illumina_humanht_12" and
"illumina_humanht_12" in the filters,

2) What version of the Illumina HT12 chip is used? This is unclear. As
for the WG6 chips it is mentioned V1,V2 or V3, HT12 have 4 versions out
so far, so which version does the information in the BiomaRt correspond to?

R code:
listMarts(host="www.ensembl.org")
ensembl =  useMart("ENSEMBL_MART_ENSEMBL", host="www.ensembl.org", dataset="hsapiens_gene_ensembl")
filt = listFilters(ensembl)

filt[grep("illumina", filt[[1]], ignore.case=TRUE), ]
                           name                                     description
12  with_illumina_humanwg_6_v1               with Illumina HumanWG 6 v1 ID(s))
13  with_illumina_humanwg_6_v2                with Illumina HumanWG 6 v2 ID(s)
14  with_illumina_humanwg_6_v3                with Illumina HumanWG 6 v3 ID(s)
15    with_illumina_humanht_12                 with Illumina Human HT 12 ID(s)
125      illumina_humanwg_6_v1   Illumina HumanWG 6 V1 ID(s) [e.g. 0000940471]
126      illumina_humanwg_6_v2 Illumina HumanWG 6 V2 ID(s) [e.g. ILMN_1748182]
127      illumina_humanwg_6_v3 Illumina HumanWG 6 v3 ID(s) [e.g. ILMN_2103362]
128        illumina_humanht_12  Illumina Human HT 12 ID(s) [e.g. ILMN_1672925]


Many Thanks in advance,
Natasha


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

Re: [BioMart Users] biomaRt query

Elena Rivkin
Hi Natasha,

1. These are two different filters that give you the following options:
The first filter 'with_illumina_humanht_12' restricts the output to all
the genes with 'illumina_humanht_12' identifier. The second filter
'illumina_humanht_12' allows you to restrict your output to specific
'illumina_humanht_12' identifiers, which you need to specify.

2. It is best to address these data specific questions to the Ensembl
helpdesk: [hidden email]. I am cc'ing them in my response.

Thank you.  
Elena Rivkin, PhD
Outreach and Training Coordinator, Informatics and Bio-computing

Ontario Institute for Cancer Research
MaRS Centre, South Tower
101 College Street, Suite 800
Toronto, Ontario, Canada M5G 0A3

Tel: 647-258-4316
Toll-free: 1-866-678-6427
www.oicr.on.ca

This message and any attachments may contain confidential and/or
privileged information for the sole use of the intended recipient. Any
review or distribution by anyone other than the person for whom it was
originally intended is strictly prohibited. If you have received this
message in error, please contact the sender and delete all copies.
Opinions, conclusions or other information contained in this message may
not be that of the organization.
 





On 11-08-19 8:48 AM, "Natasha Sahgal" <[hidden email]> wrote:

>Hello,
>
>I am new to using biomaRt, and I use it via the R/Bioconductor package.
>
>However, there are some things I do not understand.
>
>1) What is the difference between: "with_illumina_humanht_12" and
>"illumina_humanht_12" in the filters,
>
>2) What version of the Illumina HT12 chip is used? This is unclear. As
>for the WG6 chips it is mentioned V1,V2 or V3, HT12 have 4 versions out
>so far, so which version does the information in the BiomaRt correspond
>to?
>
>R code:
>listMarts(host="www.ensembl.org")
>ensembl =  useMart("ENSEMBL_MART_ENSEMBL", host="www.ensembl.org",
>dataset="hsapiens_gene_ensembl")
>filt = listFilters(ensembl)
>
>filt[grep("illumina", filt[[1]], ignore.case=TRUE), ]
>                           name
>description
>12  with_illumina_humanwg_6_v1               with Illumina HumanWG 6 v1
>ID(s))
>13  with_illumina_humanwg_6_v2                with Illumina HumanWG 6 v2
>ID(s)
>14  with_illumina_humanwg_6_v3                with Illumina HumanWG 6 v3
>ID(s)
>15    with_illumina_humanht_12                 with Illumina Human HT 12
>ID(s)
>125      illumina_humanwg_6_v1   Illumina HumanWG 6 V1 ID(s) [e.g.
>0000940471]
>126      illumina_humanwg_6_v2 Illumina HumanWG 6 V2 ID(s) [e.g.
>ILMN_1748182]
>127      illumina_humanwg_6_v3 Illumina HumanWG 6 v3 ID(s) [e.g.
>ILMN_2103362]
>128        illumina_humanht_12  Illumina Human HT 12 ID(s) [e.g.
>ILMN_1672925]
>
>
>Many Thanks in advance,
>Natasha
>
>
>_______________________________________________
>Users mailing list
>[hidden email]
>https://lists.biomart.org/mailman/listinfo/users

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