User: jeni
jeni • 40
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Posts by jeni
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... Hi!
I am studying a group of cancer patients from which I have INDELs (from DNA fastq) and expression data (RNAseq), both from a tumoral and a normal sample for each one of them.
As I know some genes affected by potential pathogenic insertions or deletions, I would like to assess, for each patient ...
written 6 weeks ago by
jeni • 40
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... Hi!
I am trying to perform some differencial expression analysis just to know which genes present different expression levels between a normal and a tumoral samples from the same patient. I have aligned and obtained gene counts with STAR and now I am trying to use DESeq2 to find differences between ...
written 10 weeks ago by
jeni • 40
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... No, we use an absolute number of supporting reads to accept the variant. For example: if there are more than 3 supporting reads then we accept the variant. ...
written 3 months ago by
jeni • 40
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... Hi!
I have analyzed some specific structural variants in a set of different samples (originated from different patients). Now, I would like to perform some correlation between the number of those variants detected in each patient and some clinical information about them. The problem is that there a ...
written 3 months ago by
jeni • 40
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... About a method to do this with statistical soundness ...
written 5 months ago by
jeni • 40
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... Hi!
I am trying to perform a differencial expression analysis between two groups of patients. But I would like to group them taking into account two variables.
Imagine I have these data:
patient1 T1 6
patient2 T1 2
patient3 T4 2
patient4 T2 0
patient5 T3 ...
written 5 months ago by
jeni • 40
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... Ok, I see. And the purpose of that is a clearer visualization? I mean, the results of the differencial expression analysis or the clustering could be different if after performing the RMA I get the zscore, or the results should be the same but clearer to plot? ...
written 5 months ago by
jeni • 40
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... Thanks for your answer! Could you explain what do you mean by 'prior to clustering'? ...
written 5 months ago by
jeni • 40
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... Hi!
I am analyzing expression microarrays data and after reading `CEL` files I perform RMA in order to get background corrected, normalized and summarized data. I have seen that some people transform this corrected data to zscore in order to reduce noise between samples. So instead of performing th ...
written 5 months ago by
jeni • 40
• updated
5 months ago by
Kevin Blighe ♦ 71k
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... Hi!
I am trying to use bumphunter to find differencially methylated regions between two groups of samples. I have read in the user guide and some tutorials that it is recommended to use B=1000 to perform 1000 permutations when you have a high amount of samples. In my case, I am studying about 500 s ...
written 5 months ago by
jeni • 40
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