User: raya.fai

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raya.fai50
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Posts by raya.fai

<prev • 14 results • page 1 of 2 • next >
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Comment: C: Reads with ambiguous annotation
... Thank you very much! Raya ...
written 8 weeks ago by raya.fai50
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Reads with ambiguous annotation
... Hi, We have a question about the proper handing of ambiguous annotation reads when using DESeq2. In our bacterial RNAseq data there is a fraction of reads (0.5-2%) that map inconclusively to two adjacent genes (gene A and gene B). We count such reads twice, one for gene A and one for gene B. Can we ...
deseq2 written 9 weeks ago by raya.fai50 • updated 9 weeks ago by Michael Love25k
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Comment: C: Finding unchanged genes using altHypothesis = "lessAbs"
... Thank you very much for your help ...
written 17 months ago by raya.fai50
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Comment: C: Finding unchanged genes using altHypothesis = "lessAbs"
... Thank you very much for your answer.  I thought that for the not changing genes I need to use the altHypothesis parameter that also requires the lfcThreshold parameter. Am I wrong? How can I get the not changing genes without a lfcThreshold? For the changing genes I also do not want a lfcThreshold ...
written 17 months ago by raya.fai50
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Comment: C: Finding unchanged genes using altHypothesis = "lessAbs"
... Hi, I hope I can bother you with another question regarding this topic. In order to find the significantly changed genes I used: ddseq <- DESeq(ddseq) res <- results(ddseq) And in order to find the unchanged genes, as you suggest, I used: ddsNoPrior <- DESeq(ddseq, betaPrior=FALSE) resL ...
written 17 months ago by raya.fai50
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Comment: A: Finding unchanged genes using altHypothesis = "lessAbs"
... Thank you very much for your quick as always answer. Raya ...
written 17 months ago by raya.fai50
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Finding unchanged genes using altHypothesis = "lessAbs"
... Hi, I am using DESeq2 for traditional RNAseq data analysis for finding genes that their expression level changed and I am also looking for genes that their level did not change. I later take these two groups of genes are characterize each group. I wanted to ask you what is more correct for taking ...
deseq2 lessabs written 17 months ago by raya.fai50
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Comment: C: Can DEseq2 handle zero values for some genes?
... Thank you very much. Your answer was very helpful. I will try next time to ask more detailed questions. Raya ...
written 3.0 years ago by raya.fai50
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Comment: A: Can DEseq2 handle zero values for some genes?
... Thank you very much. Can I use DEseq2 if about 50% of the genes have zero counts in some of the replicates? Thanks again, Raya ...
written 3.0 years ago by raya.fai50
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Can DEseq2 handle zero values for some genes?
... Hi, I wanted to ask if DEseq2 can handle zeros for some of the gene counts?  Is it better to add 1 to all the gene counts and that way not have zeros at all for better anaylsis? Thank you very much, Raya   ...
deseq2 written 3.0 years ago by raya.fai50

Latest awards to raya.fai

Great Question 17 months ago, created a question with more than 5,000 views. For Dealing with genes that have Padj=NA
Student 17 months ago, asked a question with at least 3 up-votes. For Dealing with genes that have Padj=NA
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Dealing with genes that have Padj=NA

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