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Question: Covert MethylSet to RGChannelSet object
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gravatar for maden.sean
15 months ago by
maden.sean10
United States
maden.sean10 wrote:

Hi there,

I'm interested in converting a MethylSet back to an RGChannelSet object for purposes of preprocessing (I am using unprocessed data obtained from GEO), but I'm unsure of how to do this.

My understanding is that preprocessRaw() uses manifest info to associate idat channels with the correct array probes. I'm not aware of a function that does this in reverse. I'm thinking it should be possible to do this manually with a few for loops, but the rownames for getGreen() and getRed() matrices from the RGChannelSet are numeric identifiers. I am unsure of how to go about identifying which channels go to which array probe.

I am running minfi 1.18.6 and Bioconductor 3.3.

Thanks!

Sean

ADD COMMENTlink modified 15 months ago by Kasper Daniel Hansen6.3k • written 15 months ago by maden.sean10
2
gravatar for Kasper Daniel Hansen
15 months ago by
United States
Kasper Daniel Hansen6.3k wrote:
You can't do this. For example, you have no knowledge of the so-called out of band probes, which are probes measured in the "other" color channel than they were designed for. You are also missing control probes measurements. Perhaps it is easier for you to look at the dimensions of the RGsetEx and MsetEx in the minfiData package to see that you are missing a great deal of numbers. Best, Kasper On Wed, Aug 31, 2016 at 2:53 PM, maden.sean [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User maden.sean <https: support.bioconductor.org="" u="" 8348=""/> wrote Question: > Covert MethylSet to RGChannelSet object > <https: support.bioconductor.org="" p="" 86673=""/>: > > Hi there, > > I'm interested in converting a MethylSet back to an RGChannelSet object > for purposes of preprocessing (I am using unprocessed data obtained from > GEO), but I'm unsure of how to do this. > > My understanding is that preprocessRaw() uses manifest info to associate > idat channels with the correct array probes. I'm not aware of a function > that does this in reverse. I'm thinking it should be possible to do this > manually with a few for loops, but the rownames for getGreen() and getRed() > matrices from the RGChannelSet are numeric identifiers. I am unsure of how > to go about identifying which channels go to which array probe. > > I am running minfi 1.18.6 and Bioconductor 3.3. > > Thanks! > > Sean > > ------------------------------ > > Post tags: minfi, hm450 > > You may reply via email or visit Covert MethylSet to RGChannelSet object >
ADD COMMENTlink written 15 months ago by Kasper Daniel Hansen6.3k

Kasper,

Thanks for your reply. I was hoping that, despite the missing data, I would be able to fill in the limited data I have in order to perform normalizations that don't require the other kinds of probes and intensities. 

Sean

ADD REPLYlink written 15 months ago by maden.sean10
1
So it is theoretically possible to fill in the matrices with some numbers and lots of NAs. In general, we have not assumed the presence of NAs in the code, so that could very well end badly. If you still want to try, you need to understand the data structures in the manifest package. On Wed, Aug 31, 2016 at 3:13 PM, maden.sean [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User maden.sean <https: support.bioconductor.org="" u="" 8348=""/> wrote Comment: > Covert MethylSet to RGChannelSet object > <https: support.bioconductor.org="" p="" 86673="" #86675="">: > > Kasper, > > Thanks for your reply. I was hoping that, despite the missing data, I > would be able to fill in the limited data I have in order to perform > normalizations that don't require the other kinds of probes and > intensities. > > Sean > > ------------------------------ > > Post tags: minfi, hm450 > > You may reply via email or visit https://support.bioconductor. > org/p/86673/#86675 >
ADD REPLYlink written 15 months ago by Kasper Daniel Hansen6.3k
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