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: [email protected]. 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" <[email protected]> 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 >[email protected] >https://lists.biomart.org/mailman/listinfo/users _______________________________________________ Users mailing list [email protected] https://lists.biomart.org/mailman/listinfo/users
