User: mat.lesche

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mat.lesche70
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Germany
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2 months ago
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4 years, 2 months ago
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Posts by mat.lesche

<prev • 55 results • page 2 of 6 • next >
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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 13 months ago by mat.lesche70
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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 13 months ago by mat.lesche70
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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 13 months ago by mat.lesche70
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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 13 months ago by mat.lesche70 • updated 13 months ago by Michael Love20k
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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 16 months ago by mat.lesche70
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Comment: C: Finding the correct covariate for RNAseq experiment
... Thanks Michael. ...
written 16 months ago by mat.lesche70
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Comment: C: RNA STAR to DESeq2
... You can also have a look at featureCounts (http://bioinf.wehi.edu.au/featureCounts/). It needs a gtf as annotation input, the bam files. You can run it in pe or se. It's pretty nice and produces a table with samples as columns and genes as rows. ...
written 16 months ago by mat.lesche70
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Comment: C: Finding the correct covariate for RNAseq experiment
... Hi James, now there is. Sorry but the Submit was to early. There used to be a preview button. I realised that submit is creating the thread before it was too late. ...
written 16 months ago by mat.lesche70
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Finding the correct covariate for RNAseq experiment
... Hey, I'm running an experiment with two conditions, one is the wildtype and the other is a knock out of a gene. Each sample is from a single mouse and the samples were isolated on different days. Here is an overview Sample GT Sex Date ss11 KO male may s ...
sva deseq2 differential gene expression removebatcheffect() written 16 months ago by mat.lesche70 • updated 16 months ago by Michael Love20k
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Comment: C: Increased number of total exons in DEXSeq
... Hey, Have a look at the vignette for DEXSeq. The prepare_annotation script flattens all isoforms from the same gene into a single representation of this gene. During this process it creates exonic bins out of the overlapping exons. For example if you have gene with two isoforms and in isoform A the ...
written 21 months ago by mat.lesche70

Latest awards to mat.lesche

Popular Question 4 months ago, created a question with more than 1,000 views. For DESeq2: with multiple factors and interaction terms won't show all effects
Great Question 21 months ago, created a question with more than 5,000 views. For DESeq2: with multiple factors and interaction terms won't show all effects
Great Question 21 months ago, created a question with more than 5,000 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 3.0 years ago, created a question with more than 1,000 views. For DESeq2: with multiple factors and interaction terms won't show all effects
Popular Question 3.0 years ago, created a question with more than 1,000 views. For DESeq2: multiple factors and comparison of a main factor between samples

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