User: ATPoint
ATPoint • 0
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Posts by ATPoint
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... Dear Michael,
I think there is a little flaw in the source code of `lfcShrink` with DESe2 version 1.22.2. Given one wants to turn off the `svalue` calculation one would set `svalue=F`. Still in the code if one sets type="apeglm" the svalue will in any case be turned on without respecting the value ...
written 11 days ago by
ATPoint • 0
• updated
11 days ago by
Michael Love ♦ 23k
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... 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 3 months ago by
ATPoint • 0
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... 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 5 months ago by
ATPoint • 0
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... 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 ...
written 6 months ago by
ATPoint • 0
• updated
6 months ago by
Michael Love ♦ 23k
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... 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 ...
written 10 months ago by
ATPoint • 0
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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 20 months ago by
ATPoint • 0
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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?
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written 20 months ago by
ATPoint • 0
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... May I ask if you came to an answer to this question?
...
written 20 months ago by
ATPoint • 0
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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 20 months ago by
ATPoint • 0
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