User: yoursbassanio

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Posts by yoursbassanio

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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 4 weeks 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 4 weeks ago by yoursbassanio0 • updated 4 weeks ago by Michael Love15k
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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 5 weeks ago by yoursbassanio0
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Comment: A: Deseq2 result for a variable
... Hi , Is output from   Res <- results(dds, name="V11") and  ResultSexF <- lfcShrink(dds, coef=4) from above resultsNames(dds) same? ...
written 5 weeks ago by yoursbassanio0 • updated 5 weeks ago by Michael Love15k
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Comment: C: Deseq2 result for a variable
... Thanks Mike If I upgrade to latest Deseq2. should I need to rerun from the beginning(It took me 4 days to run Deseq2)?.  Doest contrast needs 3 argument. In my case V11 is continous data example -0.08279180 0.32866904 0.19715990 0.02425360 One more doubt: Does the below design accounts(correct ...
written 5 weeks ago by yoursbassanio0
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Deseq2 result for a variable
... Hi, The following is my deseq2 design and my commands dds <- DESeqDataSetFromHTSeqCount(sampleTable = sampleTable,directory = directory,design= ~Sex+V11+V12+V13+V14+V15+V16+V17+Visit,ignoreRank=FALSE) dds <- DESeq(dds) rld <- rlog(dds) vsd <- varianceStabilizingTransformation(dds) Wi ...
deseq2 differential expression results written 5 weeks ago by yoursbassanio0 • updated 5 weeks ago by Michael Love15k
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Comment: C: coef in dmrcate
... Thanks james for the answer. In the dmrcate manual under the cpg.annoate its as follows "coef The column index in design corresponding to the phenotype comparison."     ...
written 7 months ago by yoursbassanio0
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coef in dmrcate
... Hi All What should be the coef in cpg.annotate if my intereste is "Condition". In bumphunting the coef is 2 as it calls for the column number of designmatrix. But in dmrcate manual I saw it to be index. So is it that my coef=1? designMatrix <- model.matrix(~Condition+T1+T2+T3+T4)   designMatr ...
bumphunter methylation dmrcate epic written 7 months ago by yoursbassanio0 • updated 7 months ago by James W. MacDonald45k
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Comment: C: Controlling for confounding variables in bumphunter
... @gft219 thanks for the question and @james thanks for answer and the links.But I was unable to understand if we have multiple targets under a variable;  { sex <- factor(rep(c(“M”,”F”,”Un”), each = 2)) age <- c(30, 46, 54, 76, 13, 55) treat <- factor(rep(c("Treated","Control"), times = 3 ...
written 7 months ago by yoursbassanio0

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