User: lina.faller

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Posts by lina.faller

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DESeq2: How to find out how well the model fits the data?
... Hi all, I am using DESeq2 to calculate differentially expressed genes. Is there a good way to determine how well the model fits the data? I'd appreciate it if you could share any insight or resources. Thanks! ~Lina ...
rnaseq linear model fit dseq2 written 2.3 years ago by lina.faller0 • updated 2.3 years ago by Bio_Ram0
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Comment: C: Clarification requested for the RNAseq Gene workflow document
... Thank you, I appreciate your help with interpreting these more complex models! ...
written 2.3 years ago by lina.faller0
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Comment: C: Clarification requested for the RNAseq Gene workflow document
... Great! And if a gene has a positive log2FC in the "strain_mut_vs_wt" column, then it is upregulated in the mutant strain (because the mutant strain is listed first in the description")? ...
written 2.3 years ago by lina.faller0
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Comment: C: Clarification requested for the RNAseq Gene workflow document
... Great, thank you for the reference! The interaction terms genotypeII.conditionB and genotypeIII.conditionB give the difference between the condition effect for a given genotype and the condition effect for the reference genotype. So the "strainmut.minute15" column shows the log2FC for the mutant a ...
written 2.4 years ago by lina.faller0
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Clarification requested for the RNAseq Gene workflow document
... Hi all, I am looking at the following bioconductor document: http://www.bioconductor.org/help/workflows/rnaseqGene/#time-course-experiments Towards the end of the documents, there is a heatmap with the following title: "Heatmap of log2 fold changes for genes with smallest adjusted p value" It ref ...
rnaseq deseq2 written 2.4 years ago by lina.faller0 • updated 2.4 years ago by Michael Love25k
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Comment: C: DESeq2: how to identify confounding variable in the design matrix
... Thanks for the feedback! I went back to the experimental guys and they said I should ignore the "type" information for now because it has been assigned in a somewhat arbitrary way. Instead, the time variable is more informative (because someone actually looked at a clock to take this measurement). ...
written 2.4 years ago by lina.faller0
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Comment: C: DESeq2: how to identify confounding variable in the design matrix
... The time column is in hours (so 15.1 hrs, 15.5 hrs, etc). I have been ignoring the "type" column for now because it seemed a bit arbitrary to me. As you can see, sometimes "pretreatment" seems to correspond to 15.1 hrs and sometimes it corresponds with 112 hours. For the purpose of the design, do ...
written 2.4 years ago by lina.faller0
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Comment: C: DESeq2: how to identify confounding variable in the design matrix
... Thanks for the comment! I added more information about the experimental setup above. I wasn't involved in the experimental design but I will ask the guy who designed it for more information about the irregular time points. I believe it might have to do with the growth phase (either exponential or sl ...
written 2.4 years ago by lina.faller0
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DESeq2: how to identify confounding variable in the design matrix
... Hi all, I am having a hard time identifying confounding variables in my experimental design. As soon as I add the strain:time interaction, the model does not work anymore. Any advice would be appreciated! Edit to include more information about the experimental setup: There are two different ye ...
rnaseq deseq2 design matrix confounders written 2.4 years ago by lina.faller0
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Comment: C: DESeq2: how to interpret the
... Thanks for your advice! I actually have a few different experiments and put together a plot like this for each experiment. My wetlab colleagues were asking about how to compare the different experiments using this plot and if I could calculate R-squared values or something similar. Are the rlog-tra ...
written 2.4 years ago by lina.faller0

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Popular Question 2.3 years ago, created a question with more than 1,000 views. For DESeq2: how to interpret the heatmap clustering samples

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