When we look at the filters of ensembl in biomart package in R, it shows two options for the microarray platform hg_u133a:
affy_hg_u133a: Affy hg u133a probeset ID(s) [e.g. 200874_s_at]
with_affy_hg_u133a: with Affymetrix Microarray hg u133a probeset ID(s)
the same happens for other microarrays.
The code to get filters is shown bellow:
library(biomaRt)
ensembl = useMart(biomart ="ENSEMBL_MART_ENSEMBL",dataset="hsapiens_gene_ensembl")
filters = listFilters(ensembl)
Does someone know what is the difference between affy_hg_u133a and with_affy_hg_u133a?
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written
by
salamandra
2 answers
Just to add to Emily's answer, the way you use these two filters will be quite different.
If you have a list of Affy IDs and want to know what they target, you should use affy_hg_u133a. Alternatively, if you have an existing set of genes or a genomic region, and you want to find the subset of genes that are targeted by the U133A platform, you want to use with_affy_hg_u133a.
This is discussed very briefly in the biomaRt vignette section 7.2 here
affy_hg_u133a asks you to specify a list of Affy hg 133a probseset IDs. It will find all the genes that match up to those particular IDs.
with_affy_hg_u133a does not need you to specify a list. It will find all genes that happen to have an Affy hg 133a probseset ID that matches up to them.
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