User: jaime.alvarez.benayas

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Posts by jaime.alvarez.benayas

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Deseq2 default Cooks distance threshold
... Hello, I have seen various posts regarding Cooks distance for outlier detection, but I couldn't see how to determine what is the actual cuttoff value used? Also, is it on a per gene basis or the same for all genes?   So I am running a Log Ratio Test accounting for batch: dds.LRT <- DESeq(dds ...
deseq2 outliers cookscutoff written 4 months ago by jaime.alvarez.benayas0 • updated 4 months ago by Michael Love20k
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Comment: A: Deseq multifactor test design full rank error and how to determine one variable
... Thank you for your input Michael. I have given it some thought, as you say because of the confounding one can't test simultaneously for disease, marker and batch. Additionally, something I hadn't taken into account is that the healthy samples are replicates from the same donor.id see "donor.id" colu ...
written 9 months ago by jaime.alvarez.benayas0
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Deseq multifactor test design full rank error and how to determine one variable only effect.
... Hello, I am trying to perform some test to see differential counts for different combinations of variables within an experiment. I have 26 samples divided into "condition" (disease/healthy), additionally there is a "marker" which can be either "plus" or "minus" for healthy samples and "other" for ...
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ATAC-seq: Sample size when pooling sample reads to call peaks
... Hello, I am trying to perform differential ATAC-seq on two conditions with 22 and 5 samples. My plan is to call consensus peaks by merging all the samples reads, then counting the 5' of each sample in each peak and performing DeSeq2 differential binding. However, when it comes to merging all the sa ...
sample size atac-seq peak normalize written 10 months ago by jaime.alvarez.benayas0

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