lumi: how to get number of beads information?
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krishna312 • 0
@krishna312-6866
Last seen 6.2 years ago
Finland

Hi,

I would like to get number of beads used to summarize intensity in infinium methylation 450k data and remove intensities based on less than 3 beads.

I can easily get that information using minfi as follows,

nbeads <- assayData(RGset)$NBeads

How can do that in lumi?

Further, I noticed that number of features are different in MethyLumiM and RGChannelSetExtended classes for same data. Why is it so?

> a
RGChannelSetExtended (storageMode: lockedEnvironment)
assayData: 622399 features, 13 samples
  element names: Green, GreenSD, NBeads, Red, RedSD

> MethyLumiM
MethyLumiM (storageMode: lockedEnvironment)
assayData: 485512 features, 13 samples
  element names: detection, exprs, methylated, unmethylated

I will appreciate for any help here!

Thanks!

best wishes,

Krishna

 

lumi minfi • 834 views
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@kasper-daniel-hansen-2979
Last seen 6 days ago
United States
an RGChannelSet has one row per probe. Some CpG loci are measured using two probes per loci. You therefore have more rows than you have CpG loci. Check the number of rows in preprocessRaw(a) which now has one row per CpG. This is also explained in the manual. Best, Kasper On Mon, Jul 4, 2016 at 5:18 PM, krishna312 [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User krishna312 <https: support.bioconductor.org="" u="" 6866=""/> wrote Question: > lumi: how to get number of beads information? > <https: support.bioconductor.org="" p="" 84633=""/>: > > Hi, > > I would like to get number of beads used to summarize intensity in > infinium methylation 450k data and remove intensities based on less than 3 > beads. > > I can easily get that information using minfi as follows, > > nbeads <- assayData(RGset)$NBeads > > How can do that in lumi? > > Further, I noticed that number of features are different in MethyLumiM and > RGChannelSetExtended classes for same data. Why is it so? > > > a > RGChannelSetExtended (storageMode: lockedEnvironment) > assayData: 622399 features, 13 samples > element names: Green, GreenSD, NBeads, Red, RedSD > > > MethyLumiM > MethyLumiM (storageMode: lockedEnvironment) > assayData: 485512 features, 13 samples > element names: detection, exprs, methylated, unmethylated > > I will appreciate for any help here! > > Thanks! > > best wishes, > > Krishna > > > > ------------------------------ > > Post tags: lumi, minfi > > You may reply via email or visit lumi: how to get number of beads information? >
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Thanks for pointing that out!

However, I am still looking for answer regarding getting information about number of beads used for summarizing intensities in lumi (analogous to "nbeads <- assayData(RGset)$NBeads in minfi").

best wishes,

Krishna

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