User: mat.lesche

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mat.lesche20
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Germany
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Posts by mat.lesche

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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 4 weeks ago by mat.lesche20
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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 4 weeks ago by mat.lesche20
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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 4 weeks ago by mat.lesche20
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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 4 weeks ago by mat.lesche20
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Comment: C: lfcShrink and factors with multiple levels
... That explains it. I only noticed it in version 1.16 ...
written 4 weeks ago by mat.lesche20
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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 4 weeks ago by mat.lesche20
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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 4 weeks ago by mat.lesche20
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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 4 weeks ago by mat.lesche20
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lfcShrink and factors with multiple levels
... Hello Michael, So far I have used DESeq 2 with betaPrior = T in the DESeq() function but now I'm testing it with betaPrior = False and using lfcShrink either with the coef or contrast parameter (DESeq2 version 1.18.0). I notice a couple of things which I think need clarifcation I used a fairly com ...
deseq2 relevel lfcshrink written 4 weeks ago by mat.lesche20 • updated 4 weeks ago by Michael Love15k
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Comment: C: using paired end and single end data in featurecounts
... Or merge in R would work as well. But I would remove the chromosom, start, end, strand and length column in the two dfs. new_df <- merge(table1_df, table2_df, by.x = 'Geneid', by.y = 'Geneid') ...
written 4 months ago by mat.lesche20

Latest awards to mat.lesche

Popular Question 20 months ago, created a question with more than 1,000 views. For DESeq2: multiple factors and comparison of a main factor between samples
Popular Question 2.0 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 2.0 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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