User: yoursbassanio

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Posts by yoursbassanio

<prev • 16 results • page 1 of 2 • next >
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Comment: A: DMRcate: Cpgids in DMR
... There would be multiple ways(more efficient way ) to what do than the below script which I have used solve my own problem. But It would be great to know If there is any efficient way to do the same. **OBJECT** <- is the last object from which beta/mvalue for DMRCate is give as input ...
written 12 days ago by yoursbassanio0
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Comment: A: DMRcate: Cpgids in DMR
... gr <- granges(OBJECT) locs.ranges<-names(gr[seqnames(gr) == "chr6" & start(gr)>=31539539 & end(gr) <=31540750 ]) The above two lines I was able to subset the ids belonging to 1 location of interest. But now How can I loop this for multiple locations present in a dat ...
written 12 days ago by yoursbassanio0
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Comment: C: DMRcate: Cpgids in DMR
... gr <- granges(OBJECT) locs.ranges<-names(gr[seqnames(gr) == "chr6" & start(gr)>=31539539 & end(gr) <=31540750 ]) The above two lines I was able to subset the ids belonging to 1 location of interest. How can I loop this for multiple locations present in a data.frame ...
written 12 days ago by yoursbassanio0
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DMRcate: Cpgids in DMR
... The below is my Dmrcate run and I do get the DMRS. but how to get the CPGids that are part of these DMRS corfit <- duplicateCorrelation(myMs, design=designMatrix, block = biolrep) dmrCate.<-cpg.annotate("array", myMs, what="M", arraytype = "EPIC", analysis.type="differential", design= ...
annotation methylation dmrcate epic written 13 days ago by yoursbassanio0 • updated 11 days ago by James W. MacDonald51k
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Comment: C: DMRcate liftover to grch38
... Thanks this works for me ...
written 13 days ago by yoursbassanio0
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Comment: C: DMRcate liftover to grch38
... Thanks this works for me ...
written 13 days ago by yoursbassanio0
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DMRcate liftover to grch38
... I like to run QTL analysis using Matrixeqtl on the normalized beta values from my epic array to the genotypes of the same samples. The issue is epic array data run ( Minfi & DMRcate )is based on IlluminaHumanMethylationEPICanno.ilm10b4.hg19 and the Genotype is based on Grch38. How could I ...
dmrcate hg19 liftover matrixeqtl written 4 months ago by yoursbassanio0 • updated 4 months ago by James W. MacDonald51k
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Comment: C: Deseq2: padj value changes with varying alpha
... Hi Mike, Thank you for the reply Sorry I didn't understand your answer completely. If I change my FDR from 5%(0,05) to 1% (0.01) how does it affect tthe adjusted p-value(q-value) of the same gene which had cleared in both occasion.  As show above p-value for the same gene was (2.05E-12) in both o ...
written 24 months ago by yoursbassanio0
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Deseq2: padj value changes with varying alpha
... Hi, I was running for Deseq2 on the same set of genes and samples with varying alpha as shown below. Why do adjust p-value changes for the same gene when alpha changes, even though the pvalue remains same? I thought the alpha is the fdr cutoff and the "NA" means that it didn't cleared the FDR cut ...
rnaseq deseq2 counts written 24 months ago by yoursbassanio0 • updated 24 months ago by Michael Love25k
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Comment: C: Deseq2 result for a variable
... Hi Mike, I think I found why it was taking this much time. Firstly because of rlog transformation (I have 300+ samples) and I have changed the rlog to vst. Secondly I was not using parallel(multicore). I fixed  both of them. I have filtered the gene counts outside the deseq2. One more doubt AB & ...
written 2.0 years ago by yoursbassanio0

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