User: Noa Henig

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Noa Henig50
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5 years, 8 months ago
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5 years, 9 months ago
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Posts by Noa Henig

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Comment: C: DESeq2 high fold change values for comparison of samples with zero counts
... Hi Michael, I am working on an a new setup that follows the design you suggested, should have the results soon. Meanwhile I wanted to get a quick estimate for the differential expression only in one of the cell types but I still have a problem with high fold change for samples having zero or very lo ...
written 5.7 years ago by Noa Henig50
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DESeq2 high fold change values for comparison of samples with zero counts
... Hi DESeq developers, I am running DESeq2 1.2.8 to receive differential expression in 2 different cell types. For each cell type I have control samples, over-expression of gene A, and over-expression of gene B, while the second cell type is used in order to support the findings from the first cell ty ...
regression deseq deseq2 written 5.7 years ago by Noa Henig50 • updated 5.7 years ago by Michael Love25k
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Comment: C: DESeq2 high fold change values for comparison of samples with zero counts
... Hi Simon, I forgot to mention that the counts are the *normalized* counts, I guess this is the reason you asked for the size factors. I ran DESeq2 again using the code below (this time with beta prior = FALSE to handle the issue of zeros and low counts I originally had). The fold change in this run ...
written 5.8 years ago by Noa Henig50
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Comment: C: DESeq2 high fold change values for comparison of samples with zero counts
... Hi Mike, Thanks for your prompt reply, it's a great help. I found out the version I used was 1.2.2 so I will run it again after updating to the recent version. I noticed another issue with the fold change values, which are higher than I would expect, for example: genes having these counts T0: 29852 ...
written 5.8 years ago by Noa Henig50
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DESeq2 high fold change values for comparison of samples with zero counts
... Hi, I am using DESeq2 to get differential expression of 45 samples which represent 26 different conditions. I read that the calculation of the fold change in changed DESeq2 and affects the genes having low counts more than the highly expressed genes. However, I found genes that had zero counts in se ...
deseq2 written 5.8 years ago by Noa Henig50 • updated 5.8 years ago by Michael Love25k

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Popular Question 5.7 years ago, created a question with more than 1,000 views. For DESeq2 high fold change values for comparison of samples with zero counts
Popular Question 5.7 years ago, created a question with more than 1,000 views. For DESeq2 high fold change values for comparison of samples with zero counts

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