User: mariakarand

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mariakarand10
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Norway
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3 years, 2 months ago
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4 years ago
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Posts by mariakarand

<prev • 8 results • page 1 of 1 • next >
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Comment: C: Differential expression analysis of already normalized sequence counts
... Thank you so much. I will try this. I'm aware that total count normalization is highly discouraged by bioinformaticians. However, from what I can tell DESeq's normalization method is based on the assumption that most genes are not DE and I'm not so sure I can use that assumption in my dataset. I am ...
written 3.3 years ago by mariakarand10
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Comment: C: Differential expression analysis of already normalized sequence counts
... Thanks Michael for your reply. Forgive me, but I'm not a bioinformatician, so I have to ask you to clearify: I have performed a total count normalization (divided each count by the total count in that library and multiplied it by the average total count for the whole library). Will using the sizeF ...
written 3.3 years ago by mariakarand10
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Comment: C: Differential expression analysis of already normalized sequence counts
... Because I'm not really looking at differential expression, I'm looking at microRNA stability in formalin-fixed paraffin embedded tissue compared to matched fresh frozen tissue. I fear that the normalization method in DESeq2 makes some assumptions that are based on biological differential expression ...
written 3.3 years ago by mariakarand10
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Differential expression analysis of already normalized sequence counts
... Hi, We have been using DESeq2 for differential expression analysis previously. On the dataset I'm working on (microRNA expression), I don't want to use the normalizing method implemented in the DESeq2 package. I have therefore normalized the dataset myself. Is there any way to use DESeq2 for differ ...
normalization deseq2 differential expression written 3.3 years ago by mariakarand10 • updated 3.3 years ago by Michael Love25k
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Setting a good lfcThreshold-value in DESeq2 to find stably expressed microRNAs
... Hi, We have been applying lfcThreshold test in DESeq2 with altHypotesis=lessAbs to find what microRNAare significantly stably expressed between matched fresh frozen and formalin-fixated paraffin-embedded tissue. In the official manual, they use lfcThreshold=0.5. When we use the same threshold, we d ...
microrna ffpe deseq2 stable expression lfcthreshold written 4.0 years ago by mariakarand10 • updated 4.0 years ago by Michael Love25k
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Comment: C: How to find significantly stably expressed miRNA with DESeq2 DE results
... Thanks! A follow-up question: Is there any key to find what threshold you should use, or do you generally recomend a treshold -value of abs(0.3)? And in the R-script it's first written theta <- .3 But the "theta" is never used again, rather "thr" is used in the Z-tests. Is this a typo? Is "t ...
written 4.0 years ago by mariakarand10
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Answer: A: How to find significantly stably expressed miRNA with DESeq2 DE results
... Thanks! A follow-up question: Is there any key to find what threshold you should use, or do you generally recomend a treshold -value of abs(0.3)? And in the R-script it's first written theta <- .3 But the "theta" is never used again, rather "thr" is used in the Z-tests. Is this a typo? Is "t ...
written 4.0 years ago by mariakarand10
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How to find significantly stably expressed miRNA with DESeq2 DE results
... Hi, I'm working with DESeq2 DE results of microRNA expression (which I have not myself performed). I want to identify both differentially expressed miRNA and significantly stably expresssed miRNA. The DE miRNAs are obviously the miRNA with p<0.05. How can I identify stably expressed miRNAs from ...

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Popular Question 3.2 years ago, created a question with more than 1,000 views. For How to find significantly stably expressed miRNA with DESeq2 DE results
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Setting a good lfcThreshold-value in DESeq2 to find stably expressed microRNAs

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