User: poojitha.stemcell

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Posts by poojitha.stemcell

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Comment: C: DMRcate results cg ID of significant DMR
... Its not a surprise that it is such a small thing that gives error. Thank you Tim. The codes are working now.  Cheers! Poojitha ...
written 5 days ago by poojitha.stemcell0
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Comment: C: DMRcate results cg ID of significant DMR
... Hi Tim, I have been using this code for a while now and it always worked for me and returned the CpGs constituting the DMRs. However, when I tried to use it today, locs turns out empty and the same with loc.ranges. I switched to using another function (makeGRanges) in package humarray. I used the a ...
written 6 days ago by poojitha.stemcell0
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Comment: C: Error using read.metharray.exp in minfi to read idat files
... Thank you Andy and Kasper. I tried renaming the Sentrix ID and position columns and added full path to Basename column. It seems to work now. #Problemresolved ...
written 22 days ago by poojitha.stemcell0
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Answer: A: Error using read.metharray.exp in minfi to read idat files
... My Samplesheet looks like this: > head(samplesheet_blood)   SampleName   cell_type    chip.ID chip.C0.position chip.Row.Pos          Basename 1     WB 105 Whole blood 5684819001              C01          R01 5684819001_R01C01 2     WB 218 Whole blood 5684819001              C01          R02 5684 ...
written 27 days ago by poojitha.stemcell0
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Comment: C: minfi - estimatecellcount function
... I have the same problem. Evrything worked fine until yesterday and today I get the following error message when I try to use preprocessFunnorm function in minfi (see below in bold). I have tried the first 2 fixes you suggested (no luck!). Are you able to think of anything else? Regards, Poojitha ...
written 27 days ago by poojitha.stemcell0
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Comment: C: Error using read.metharray.exp in minfi to read idat files
... I get the same error even after correcting it all to zeros.  ...
written 27 days ago by poojitha.stemcell0
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Error using read.metharray.exp in minfi to read idat files
... Hi, I have been using minfi to process Illumina 450K. I have never faced any issues with reading in IDAT files using read.metharray.exp() function with a valid samplesheet input that includes a column 'Basename' containing the barcodes of IDAT files. However, when I tried to do the same today, I am ...
minfi idat read.metharray.exp hm450k written 28 days ago by poojitha.stemcell0
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Answer: A: Is it possible to convert Methylumi object into RGChannelSet
... 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 ...
written 6 weeks ago by poojitha.stemcell0
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probeFiltering function on RGChannelset
... 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 an ...
minfi dnamarray probefiltering written 4 months ago by poojitha.stemcell0 • updated 14 days ago by negusse0
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FuntooNorm on 450K and Epic data combined RGSet
... I am trying to perform funtooNorm on a RGSet object, that has samples run on 450K and EPIC arrays. I combined the two objects using combineArrays function in minfi. I am able to perform funtooNorm on 450K data object separately, but not on EPIC data or combined data object. I get the following error ...
minfi illuminahumanmethylationepicanno.ilmn10b.hg19 funtoonorm written 5 months ago by poojitha.stemcell0 • updated 5 months ago by Kasper Daniel Hansen6.3k

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