User: mat.lesche

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mat.lesche70
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Posts by mat.lesche

<prev • 56 results • page 2 of 6 • next >
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Comment: C: lfcShrink and factors with multiple levels
... That explains it. I only noticed it in version 1.16 ...
written 23 months ago by mat.lesche70
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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 23 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 23 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 23 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 23 months ago by mat.lesche70 • updated 23 months ago by Michael Love25k
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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 2.2 years ago by mat.lesche70
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Comment: C: Finding the correct covariate for RNAseq experiment
... Thanks Michael. ...
written 2.2 years 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 2.2 years 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 2.2 years 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 2.2 years ago by mat.lesche70 • updated 2.2 years ago by Michael Love25k

Latest awards to mat.lesche

Student 12 months ago, asked a question with at least 3 up-votes. For DESeq2: removing levels from a factor or not having them in the analysis at all
Popular Question 12 months ago, created a question with more than 1,000 views. For lfcShrink and factors with multiple levels
Popular Question 12 months ago, created a question with more than 1,000 views. For Design and independent filtering of patient RNA-seq data
Popular Question 14 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 2.6 years ago, created a question with more than 5,000 views. For DESeq2: multiple factors and comparison of a main factor between samples
Great Question 2.6 years 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 3.5 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 3.8 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 3.8 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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