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User: ATPoint

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ATPoint0
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Posts by ATPoint

<prev • 8 results • page 1 of 1 • next >
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Comment: C: Unexpected MAplot after apeglm shrinkage in DESeq2
... Thank you. Just out of interest, because I encountered this problem also on a different and unrelated dataset with larger sample sizes, suggesting that this is a rather general issue when n becomes large. Do you plan to make changes in future versions of `apeglm` to compensate for this issue interna ...
written 28 days ago by ATPoint0
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Comment: C: DESeq2 MA plot normalisation Issue
... You should at least provide the MA plot and some data to reproduce what you've stated in the question. The DESeq2 object saved in a rdata file would be an option. ...
written 3 months ago by ATPoint0
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Unexpected MAplot after apeglm shrinkage in DESeq2
... Dear Michael, I am analyzing an RNA-seq cohort of about 90 patients for differential expression between two disease subtypes. Low-level processing was done with Salmon/tximport followed by the standard workflow with DESeq2, using the disease subtype as the only covariate in the design. I was quiet ...
deseq2 rna-seq apeglm written 3 months ago by ATPoint0 • updated 3 months ago by Michael Love21k
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Significant reporter activity with mpralm function
... Good morning, the mpra package seems promising to perform differential analysis of massively-parallel reporter assays between conditions, be it genotypes/alleles, tissues or treatments. The comparison takes RNA and DNA counts for both conditions into account and tests for significant differences. S ...
linear model mpra mpralm reporter assay written 8 months ago by ATPoint0
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Comment: C: Normalization in DESeq2
... Here is the plot. It is not RNA-seq but a NGS-based reporter assay for certain regulatory elements. The two samples have quiet different readcounts (factor 3). Would you say I can use DESeqs estimated size factors here? ...
written 18 months ago by ATPoint0
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Comment: C: Normalization in DESeq2
... Thanks for the reply. What I meant is if there is a metric that can be calculated in order to decide if "the median ratio captures the scaling factor from the non-DE genes". The MA-plot is supposed to show the "bulk of genes on the x-axis", but is there any threshold beyond looking at it by eye? ...
written 18 months ago by ATPoint0
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Comment: C: Differential binding of ATAC-seq data with no replicates
... May I ask if you came to an answer to this question? ...
written 18 months ago by ATPoint0
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Comment: C: Normalization in DESeq2
... Even though this post is > 2 years old, maybe you can still comment on the following: Is there a metric or any kind of threshold that one can calculate based on the MA-Plot in order to decide if: 1) "enough" data points are shared between conditions and 2) normalization is necessary and benefic ...
written 18 months ago by ATPoint0

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