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Guido Hooiveld
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@guido-hooiveld-2020
Last seen 3 hours ago
Wageningen University, Wageningen, the …
Hello,
I would like to extract the probes that belong to a set of probesets
from a PdInfo database, but despite searching the archives I got
stuck... I would appreciate some hints.
To be specific: I am working with an Affymetrix miRNA 3.1 dataset. I
would like to extract all probes that belong to e.g. a set of affy
control probesets, such as e.g. AFFX-BkGr17-GC10_st and AFFX-
BkGr17-GC11_st.
This is my approach:
> library(pd.mirna.3.1)
> con <- db(pd.mirna.3.1)
> affy.probesets <- c("AFFX-BkGr17-GC10_st","AFFX-BkGr17-GC11_st")
> affy.probesets
[1] "AFFX-BkGr17-GC10_st" "AFFX-BkGr17-GC11_st"
>
> #check available tables/information
> dbGetQuery(con, "select name, sql from sqlite_master where
type='table'")
name
sql
1 type_dict
CREATE TABLE type_dict (type INTEGER PRIMARY KEY, type_id TEXT)
2 featureSet CREATE TABLE featureSet (fsetid INTEGER PRIMARY
KEY, man_fsetid TEXT, type INTEGER REFERENCES type_dict(type))
3 pmfeature CREATE TABLE pmfeature (fid INTEGER, fsetid INTEGER
REFERENCES featureSet(fsetid), atom INTEGER, x INTEGER, y INTEGER)
4 mmfeature CREATE TABLE mmfeature (fid INTEGER, fsetid INTEGER
REFERENCES featureSet(fsetid), atom INTEGER, x INTEGER, y INTEGER)
5 table_info
CREATE TABLE table_info \n( tbl TEXT,\n\trow_count INTEGER \n)
>
So far so good.
However, how now to continue?
For arrays for which a CDF is available, for e.g. the miRNA 1.0 array
I would do something like this (although now only the probes for the
1st probeset in affy.probesets would be extracted, but that's now not
the main question) :
> get(affy.probesets, mirna10cdf)
pm mm
[1,] 34705 NA
[2,] 46085 NA
[3,] 20445 NA
[4,] 26368 NA
<<snip>>
Main question: how could I achieve this when using a PdInfo object?
Related to this, how can I get more info on what the various keys
represent? E.g. what does 'man_fsetid' represent?
[From the mailing list I meanwhile now these represent the Affymetrix
"probeset_name", and the 'fsetid' the Affymetrix "probeset_id"].
-->> Reason I am asking all this is because I would like to analyze
(normalize) my miRNA 3.1 dataset using the normexp-by-control
background correction (nec function in limma), essentially as
described in:
http://www.pubmed.org/23709276.
Thanks,
Guido
---------------------------------------------------------
Guido Hooiveld, PhD
Nutrition, Metabolism & Genomics Group
Division of Human Nutrition
Wageningen University
Biotechnion, Bomenweg 2
NL-6703 HD Wageningen
the Netherlands
tel: (+)31 317 485788
fax: (+)31 317 483342
email: guido.hooiveld@wur.nl
internet: http://nutrigene.4t.com
http://scholar.google.com/citations?user=qFHaMnoAAAAJ
http://www.researcherid.com/rid/F-4912-2010
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