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Question: Log-Transform Values of eSet
0
gravatar for bi_Scholar
13 months ago by
bi_Scholar0
bi_Scholar0 wrote:

Hello,

I downloaded a GSE file from GEO and converted it to an expression-set using GEOquery. However, even though the values are normalized, they are not log-transformed which is kind of bad, since I'm using limma to analyse the samples.

Is it possible to log-transform the values of an eSet directly (without using exprs()), or can I tell limma to log-transform the values while using fit() or topTable()?

ADD COMMENTlink modified 13 months ago by svlachavas570 • written 13 months ago by bi_Scholar0
1
gravatar for bi_Scholar
13 months ago by
bi_Scholar0
bi_Scholar0 wrote:

Well, I think I have found the solution, sorry for bothering you guys.

exprs(eSet) <- log2(exprs(eSet))
 

 

ADD COMMENTlink modified 13 months ago • written 13 months ago by bi_Scholar0
0
gravatar for svlachavas
13 months ago by
svlachavas570
Greece/Athens/National Hellenic Research Foundation
svlachavas570 wrote:

Dear bi_Scholar,

what platform is your dataset of interest ? and also what specific functions you have used? It is a bit weird you mention that the values are normalized but not log-transformed (but of course it depends on the normalization methodology).

Anyway, personally i think the simplest way is to download the raw data by using the function:

getGEOSuppFiles("GSE...")

Best,

Efstathios

ADD COMMENTlink written 13 months ago by svlachavas570

Hello svlachavas,

I'm using the Illumina GPL8432 platform. The Data is quantile-normalized but not log2-transformed.
As mentioned above, I manually log2-transformed the normalized values in order to use limma. Is this a bad thing?

 

Thanks for taking your time,

M

ADD REPLYlink modified 12 months ago • written 12 months ago by bi_Scholar0
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