Difference between affy_hg_u133a and with_affy_hg_u133a

Question

[salamandra]

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?

Answer 1

[Mike Smith]

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

Answer 2

[Emily]

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.