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Question: probeFiltering function on RGChannelset
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gravatar for poojitha.stemcell
4 months ago by
poojitha.stemcell0 wrote:

I came across the probeFiltering function in DNAmArray package (https://molepi.github.io/DNAmArray_workflow/04_ProbeFiltering.html), which can be used to filter out cross reactive probes, probes with bd detection p value and based on number of beads. I tried using this with my RGChannelset object and got the following error. 

Error in probeFiltering(RGSet_nooutbsxy) : 
  RGset should be of class 'RGChannelSetExtended' in order to perform filtering on number of beads!

Is there a way I can convert my RGChannelSet object to RGChannelSetExtended? I will not be able to create an RGChannelSetExtended using the read.metharray function in minfi as I am using a combination of 450k data and epic data. Is there any other solution to this problem?

Regards,

Poojitha

ADD COMMENTlink modified 17 days ago by negusse0 • written 4 months ago by poojitha.stemcell0
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gravatar for negusse
17 days ago by
negusse0
negusse0 wrote:

I have got similar problem. I have tried, if you set extend = TRUE, it will generate RGChannelSetExtended object. 

read.metharray.exp(base = NULL, targets = NULL, extended = TRUE, recursive = FALSE, verbose = FALSE, force = FALSE)

More information  at: https://www.rdocumentation.org/packages/minfi/versions/1.18.4/topics/read.metharray.exp

 

Negusse 

 

 

ADD COMMENTlink written 17 days ago by negusse0
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