User: mat.lesche

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mat.lesche70
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Germany
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5 months, 4 weeks ago
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4 years, 11 months ago
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Posts by mat.lesche

<prev • 56 results • page 1 of 6 • next >
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Comment: C: model design in rna seq - deseq2
... Hey, It would be really helpful for us if you your text has a proper formatting. Please use code blocks for code dds <- DESeqDataSetFromMatrix(countData = counts, colData = annotation, design = ~ time+person) or add a table for your condition table and maybe some graphic from the PCA As f ...
written 5 months ago by mat.lesche70
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Comment: C: Splitting a dataset and control sample batch
... Hi Michael, Thanks for the answer. I have look at the limma-voom which will be very interesting. In the mean time, would be the following a valid approach: I try to answer the question with fixed effect with the whole data sets and question like group 2 to group 1 is done with a reduced data set th ...
written 11 months ago by mat.lesche70
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Comment: C: Splitting a dataset and control sample batch
... Yes. Sorry I meant Donor and not samples. The comparison T6_RE_Co vs T6_NR_RAP should need a the design Donor + C because the same Donors are in both Treatments. ...
written 11 months ago by mat.lesche70
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Splitting a dataset and control sample batch
... The experiment design is the following. There are two groups (NR and RE) and each comes in triplicates. These triplicates were grown on a dish. At timepoint 0 (T0) samples were collected. Afterwards, they were treated (RAP) or not (Co) and at timepoint 6 (T6), samples were collected again. Here is t ...
deseq2 interactions batch effect correction grouping variable written 11 months ago by mat.lesche70 • updated 11 months ago by Michael Love25k
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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 13 months ago by mat.lesche70
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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 13 months ago by mat.lesche70 • updated 13 months ago by Michael Love25k
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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 22 months ago by mat.lesche70
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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 22 months ago by mat.lesche70
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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 22 months ago by mat.lesche70
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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 22 months ago by mat.lesche70

Latest awards to mat.lesche

Student 11 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 11 months ago, created a question with more than 1,000 views. For lfcShrink and factors with multiple levels
Popular Question 11 months ago, created a question with more than 1,000 views. For Design and independent filtering of patient RNA-seq data
Popular Question 13 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 2.5 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 2.5 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 3.4 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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