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User: chiara.facciotto

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Posts by chiara.facciotto

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How can I compare the expression of two genes within the same sample?
... Hi, I am interested in comparing the expression of genes within the same sample and ranked them from the most expressed to the least expressed. I cannot use counts nor normalized counts because they do not take into account the gene lengths. Which measure would you suggest I use? Does DESeq2 provid ...
rnaseq deseq2 gene expression written 7 weeks ago by chiara.facciotto0 • updated 7 weeks ago by heyao30
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Conversion from counts to FPKM
... Hi, I am trying to use DESeq2 to convert raw counts to fpkm, so I can compare gene aboundance across genes and not only across samples. I have a couple of questions on how to do so: Should I first normalize the counts and transform them with vst and then use the fpkm() function, or should I simp ...
normalization deseq2 counts fpkm fpkm() written 10 weeks ago by chiara.facciotto0 • updated 10 weeks ago by Michael Love22k
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Answer: A: Data normalization and transformation using DESeq2
... Thanks! And is it ok to run estimateSizeFactors(dss) before running rlog(dds, blind=FALSE)? ...
written 11 weeks ago by chiara.facciotto0
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Data normalization and transformation using DESeq2
... Hi, I am trying to use DESeq2 to perform normalization of my RNA-Seq data. I am wondering if, after estimating the size factors, I can directly run the rlog or vst transformation, or if I also need to use the count function in between. Basically I wonder which is the correct one between option 1 or ...

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