normalization of a miRNA microarray
2
0
Entering edit mode
alptaciroglu ▴ 50
@alptaciroglu-8859
Last seen 15 months ago
Turkey

Dear All,

 

I am trying to process an affymetrix miRNA microarray that is shown to have 7815 rownames (miRNA identifiers). When I read the CEL files with ReadAffy() function :

 

RAW <- ReadAffy()

dim(exprs(RAW)) yields 52900 probes where there should be 7815. Affybatch object also says that there are 7815 genes but why expression file of the Affybatch object shows up 52900 rows ? This is dealt with in rma() normalization and there stays correctly 7815 rows but other normalization packages (vsn, ExiMiR) cannot deal with this and there remains 52900 probes after normalization. I would appreciate if you could let me know what is going on. Thanks 


With kind regards,


Alperen Taciroglu

 

normalization vsn eximir microarray miRNA • 802 views
ADD COMMENT
1
Entering edit mode
@james-w-macdonald-5106
Last seen 7 hours ago
United States

Affy arrays have multiple 25-mers that together are intended to measure a single transcript. This is silly in the case of the miRNA arrays, as the target is shorter than the oligo that is used to measure (and there are multiple identical 25-mers for each miRNA).

Anyway, that's why there are more probes before you normalize. Also note that the vsn package has a function called vsnrma() that does understand what to do with Affy arrays.

ADD COMMENT
0
Entering edit mode

It seems vsnrma() correctly returns 7815 rows. Thanks very much

ADD REPLY
0
Entering edit mode
@wolfgang-huber-3550
Last seen 5 days ago
EMBL European Molecular Biology Laborat…

What do you get from

cdfName(RAW)

Affymetrix arrays usually have multiple features (probes) per probe set (targeted gene). Could it be that 7815 is the number of probe sets and 52900 the number of probes?

 

Wolfgang

 

ADD COMMENT
0
Entering edit mode

miRNA-1_0_2Xgain I got from cdfName(RAW). I do not know the answer to your question but I think James' reply might be answer to both of us. Anyway, thanks so much for reply

ADD REPLY
0
Entering edit mode

miRNA-1_0_2Xgain I got from cdfName(RAW). I do not know the answer to your question but I think James' reply might be answer to both of us. Anyway, thanks so much for reply

ADD REPLY

Login before adding your answer.

Traffic: 439 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6