User: yuan.qing

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yuan.qing0
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Posts by yuan.qing

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how to explain the figure obtained from edgeR?
... I ploted histogram of unadjusted p-value. I encounted a huge peak at p-value=1, anybody knows the reason? Is it because the zero counts? How can I verify that? hist(top.table.edgeR$PValue, breaks=100, main="",xlab="Unadjusted P values", col="lightblue") Thanks for your help!   ...
edger unadjusted p-value written 4.1 years ago by yuan.qing0 • updated 4.1 years ago by Gordon Smyth37k
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How to modify function of samr.estimate.depth of samr
... How to modify the source code in samr? I want to do the TMM normalization. I had the following: SAMseq.test = SAMseq(countdata1, finaldata1$Group, geneid=as.character(rownames(countdata1)),                      genenames=as.character(rownames(countdata1)),                     resp.type="Two class ...
samr written 4.1 years ago by yuan.qing0 • updated 4.1 years ago by James W. MacDonald50k
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Comment: C: DESeq2 variance transformation error and plot dispersion Estimate
... Right, I renamed it to be DESeq2_1 instead of DESeq2, my mistake. Thank you very much! Another question is, do I need to filter low gene expression before inputting into DESeq2? ...
written 4.1 years ago by yuan.qing0
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DESeq2 variance transformation error and plot dispersion Estimate
... Hi,  I was trying to visualize the normalized count of my data, however, I was running into errors: normalized.count <- as.data.frame(counts(DESeq2, normalized=TRUE)) Error in as.data.frame(counts(DESeq2, normalized = TRUE)) :    error in evaluating the argument 'x' in selecting a method for f ...
deseq2 written 4.1 years ago by yuan.qing0 • updated 4.1 years ago by Michael Love24k
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Comment: C: DESeq plotting problems
... How is the data input for DESeq2?  is the same as y.DESeq<-newCountDataSet(countdata1, finaldata1$Group)  ...
written 4.1 years ago by yuan.qing0
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DESeq plotting problems
... I am using the DESeq package to do a DE analysis. I would like to plot the PCA plot and Dispersion estimates plot in r studio. However, I am running into errors. I tried to construct an DESeq specific object called CountDataSet to hold count and pheno data: y.DESeq<-newCountDataSet(countdata1, ...
deseq deseq2 written 4.1 years ago by yuan.qing0 • updated 4.1 years ago by Michael Love24k

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Popular Question 4.0 years ago, created a question with more than 1,000 views. For DESeq2 variance transformation error and plot dispersion Estimate

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