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Question: Is it possible to convert Methylumi object into RGChannelSet
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19 months ago by
poojitha.stemcell0 wrote:

I am trying to integrate over 15 datasets into one RGChannelSet in order to normalise it using the package funtoonorm. I used GEOquery to get the datasets from GEO. However, since minfi only reads IDAT files, I could not get an RGset from GEO datasets that do not have IDAT files. Hence, I had to create a methylumi object from the series matrix text file from GEO. However, funtoonorm only works with minfi object. Would any of you know if there is a way of converting methylumi object into RGset?

Thank you,

Poojitha

modified 8 months ago • written 19 months ago by poojitha.stemcell0
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19 months ago by
United States
James W. MacDonald46k wrote:

Yes, there is. See the last few pages of the methylumi vignette.

Thank you James:) I created a methylumiset object from series matrix in GEO and tried using the coercing function from methylumi vignette, but got the following error message:

> lumiMethy <- methylumiR("GSE50192_GPL13534_Matrix_raw_data.txt", sep="\t")

> rgSet450k <- as(mset450k, 'RGChannelSet')

Error in methylumiToMinfi(lumiMethy) :

Cannot construct an RGChannelSet without full (OOB) intensities

Would you know how to resolve this? Is there a way of retaining OOB intensities while creating the methylumi object?

It depends on what data the submitter sent to GEO. In the case of this particular GSE, it appears they just sent the processed beta values, and you can't convert those data to an RGChannelSet. An RGChannelSet implies that you have the original Red and Green channel data, and you can't get those values from the betas alone.

ADD REPLYlink written 19 months ago by James W. MacDonald46k
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8 months ago by
poojitha.stemcell0 wrote:

Thank you James. The data i am now dealing with is a matrix of signal intensities from GSE35069. I still get the same error of missing OOB intensities. Would you know why this is happening?

Regards,

Poojitha

Its the same issue. When you get intensities only from GEO you do not get

- control probes
- out of band probes

To get this information, you generally need the original IDAT files. This means that any algorithm which makes use of either control probes or out of band probes will fail.

ADD REPLYlink written 8 months ago by Kasper Daniel Hansen6.3k