User: mat.lesche

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mat.lesche40
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Germany
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3 years, 10 months ago
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m*********@gmail.com

Posts by mat.lesche

<prev • 52 results • page 1 of 6 • next >
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Comment: C: lfcShrink behavior with homogeneous expression dataset
... Hi Michael, Thanks, as many times before, for the feedback. After reading your tutorials and comments on threads, I understand the shrinkage. But what is a bit of a concern is providing a ma plot to a biologist. In the past the would a similar plots compared to picture 1 and 2 in https://ibb.co/fjz ...
written 15 days ago by mat.lesche40
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lfcShrink behavior with homogeneous expression dataset
... Hello, I have a small dataset with 3 replicates per condition. One condition is a gene over-expression, the other is a control. I'm used to run DESeq2 with betaPrior = True to have a comparability with the 'old' DESeq2 behavior. I can't apply this old workflow because the expression differences bet ...
deseq2 betaprior lfcshrink written 15 days ago by mat.lesche40 • updated 15 days ago by Michael Love19k
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Comment: C: lfcShrink and factors with multiple levels
... We were thinking about doing a separate analysis for DM vs DP because the samples are quite problematic when it comes to sample extraction. But I could use your shown workflow for the DP vs CO and DM vs CO. I don't really want to recommend these genes as DEGs but I like to show the change in express ...
written 9 months ago by mat.lesche40
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Comment: C: lfcShrink and factors with multiple levels
...   Co1 DP1 DP2 DM1 DM1 GeneA 0 0.859386 0.0000000 0 321.0731 GeneB 0 0.000000 0.6611592 0 535.1218 GeneC 0 0.859386 0.0000000 0 419.9690 The comparison was Co vs DP and it's a single sample vs two r ...
written 9 months ago by mat.lesche40
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Comment: C: lfcShrink and factors with multiple levels
... Hi Michael, Here are some suggestion for the documentation ?lfcShrink: "the name or number of the coefficient (LFC) to shrink, consult resultsNames(dds) after running DESeq(dds). note: only coef or contrast can be specified, not both. type="apeglm" requires use of coef." I would write something ...
written 9 months ago by mat.lesche40
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Comment: C: lfcShrink and factors with multiple levels
... This was my mistake and most likely due to copy and paste. I just ran it with 1.16 and 1.18 and it's MAP ...
written 9 months ago by mat.lesche40
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Comment: C: lfcShrink and factors with multiple levels
... That explains it. I only noticed it in version 1.16 ...
written 9 months ago by mat.lesche40
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Comment: C: lfcShrink and factors with multiple levels
... I'll have a look and report back. the lfcSE column disappears too. Also I'll write a bigger comment on how to improve the documentation. ...
written 9 months ago by mat.lesche40
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Comment: C: lfcShrink and factors with multiple levels
... Hey Michael, Thanks for the reply. Now the doc to ?lfcShrink makes more sense: "the number of the coefficient (LFC) to shrink, consult resultsNames(dds) after running DESeq(dds, betaPrior=FALSE). only coef or contrast can be specified, not both" I simply did not make the connection from the text, ...
written 9 months ago by mat.lesche40
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Comment: C: lfcShrink and factors with multiple levels
... Hi Gavin, That's exactly the point I'm trying to make. I'm aware that it is swapped. If I'm interested in DM vs DP and I define it in the results() function, I get the opposite from lfcShrink because the initial reference level is set to DM. It's even more worrying if the initial level is set to Co ...
written 9 months ago by mat.lesche40

Latest awards to mat.lesche

Great Question 17 months ago, created a question with more than 5,000 views. For DESeq2: multiple factors and comparison of a main factor between samples
Great Question 17 months ago, created a question with more than 5,000 views. For DESeq2: with multiple factors and interaction terms won't show all effects
Popular Question 2.3 years ago, created a question with more than 1,000 views. For DESeq2: multiple factors and comparison of a main factor between samples
Popular Question 2.7 years ago, created a question with more than 1,000 views. For DESeq2: multiple factors and comparison of a main factor between samples
Popular Question 2.7 years ago, created a question with more than 1,000 views. For DESeq2: with multiple factors and interaction terms won't show all effects

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