User: jeni

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jeni40
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1 month ago
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Posts by jeni

<prev • 53 results • page 1 of 6 • next >
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How to statistically determine if a mutation has an impact on expression individually for one patient
... 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 ...
variant calling rna-seq written 6 weeks ago by jeni40
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(Closed) Differential expression between just 2 samples: a normal and a tumour sample from the same patient
... 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 ...
rna-seq written 10 weeks ago by jeni40
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Comment: C: Correct number of detected variants by coverage
... 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 jeni40
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Correct number of detected variants by coverage
... 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 ...
variant calling written 3 months ago by jeni40
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Comment: C: Differencial expression analysis between groups determined by two variables
... About a method to do this with statistical soundness ...
written 5 months ago by jeni40
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Differencial expression analysis between groups determined by two variables
... 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 ...
expression microarray clustering written 5 months ago by jeni40
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Comment: C: Does it make sense to transform expression data to zscore after performing RMA?
... 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 jeni40
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Comment: C: Does it make sense to transform expression data to zscore after performing RMA?
... Thanks for your answer! Could you explain what do you mean by 'prior to clustering'? ...
written 5 months ago by jeni40
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Does it make sense to transform expression data to zscore after performing RMA?
... 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 ...
expression microarray written 5 months ago by jeni40 • updated 5 months ago by Kevin Blighe71k
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Is it right to use a low amount of bumphunter permutations?
... 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 ...
methylation microarray dmr written 5 months ago by jeni40

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