User: raya.fai

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raya.fai20
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Posts by raya.fai

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Comment: C: Finding unchanged genes using altHypothesis = "lessAbs"
... Thank you very much for your help ...
written 12 months ago by raya.fai20
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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 12 months ago by raya.fai20
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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 12 months ago by raya.fai20
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Comment: A: Finding unchanged genes using altHypothesis = "lessAbs"
... Thank you very much for your quick as always answer. Raya ...
written 12 months ago by raya.fai20
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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 12 months ago by raya.fai20
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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 2.5 years ago by raya.fai20
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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 2.5 years ago by raya.fai20
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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 2.6 years ago by raya.fai20
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Answer: A: Using DEseq with IP vs. total RNA
... Thank you very much for you quick answer. I have 3 replicates. Raya ...
written 3.3 years ago by raya.fai20
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Using DEseq with IP vs. total RNA
... Hello, I would like to ask whether I can use DEseq2 for the analysis of total RNA as group 1 and RNA from riboprotein IP as group 2, both from the same condition. I am interested in finding genes that are enriched in the IP.   Thank you, Raya ...
deseq2 ip written 3.3 years ago by raya.fai20

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Popular Question 2.5 years ago, created a question with more than 1,000 views. For Dealing with genes that have Padj=NA

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