User: Jonas B.

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Jonas B.0
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Posts by Jonas B.

<prev • 20 results • page 2 of 2 • next >
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Comment: C: LFC shrinkage executed when not expected (DESeq2)
... Dear Michael, I've been experimenting with the group function a bit more, on a simpeler data set. The experiment had the following design: three treatments: control, mild, severe three zones: mer, elo, mat To test specific combinations of both factors, the manual advices to do the following: ...
written 20 months ago by Jonas B.0
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Comment: C: LFC shrinkage executed when not expected (DESeq2)
... Dear Michael, Thank you so much for your time and response. I do believe that I understand the the mistake we're making.  And indeed, our design is complex enough to solicit somebody with more experience in this topic. I will only return to the forum with more precise questions or when unexplainab ...
written 20 months ago by Jonas B.0
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Comment: C: LFC shrinkage executed when not expected (DESeq2)
... Dear Michael,   Thank you for your response.   We got confused with the different methods to analyse specific contrasts. Following the manual, we've now decided to do the following: For any three-way contrasts of interest, we believe that we have to follow the interaction instructions (manual) ...
written 20 months ago by Jonas B.0
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Comment: C: LFC shrinkage executed when not expected (DESeq2)
... Dear Michael, Thank you for your quick response. It turns out that my version is outdated. I really didn't expect this, since I've only installed it in December 2017. Having looked into this, I've noticed that an older version was installed because I'm running an older R-version. I didn't know thi ...
written 20 months ago by Jonas B.0
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LFC shrinkage executed when not expected (DESeq2)
... Dear all,   While trying to obtain specific LFCs, we noticed an inconsistency in the results.   We are performing a RNAseq analysis of an experiment with three fixed factors: treatment (control, CL), genotype (G1, G2, G3) and time (t0, t1, t2). We are interested in specific comparisons, for ins ...
deseq2 written 20 months ago by Jonas B.0
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Comment: C: Are two biological replicates enough for a transcriptome analysis using DESeq2?
... Dear Sean, Thank you for your quick response and for noting the possibility of removing biological variation by removing outliers based on a PCA. To respond to your suggestion about the outliers: The effect of sampling zone in the leaf is quite dominant and these two samples did not match there zo ...
written 20 months ago by Jonas B.0
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Are two biological replicates enough for a transcriptome analysis using DESeq2?
... Hi all,   We are performing a transcriptome analysis with DESeq2. We have three factors: treatment (control and drought), climate (CO2 and ambient) and zone in the leaf (zone1, zone2, zone3). For each possible combination, we have 3 biological replicates (no technical replicates). The PCA showed ...
deseq2 written 20 months ago by Jonas B.0 • updated 20 months ago by Sean Davis21k
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Comment: C: TWO-way analysis with DESeq2 - obtaining p-values for the fixed factors and the
... Hi Michael,   Thank you for the quick response. Everything is clear now. Concerning the second question, I should have checked the FAQ first. My apologies!  Thank you for your time and help!   Kind regards and happy holidays, Jonas ...
written 22 months ago by Jonas B.0
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Comment: C: TWO-way analysis with DESeq2 - obtaining p-values for the fixed factors and the
... Hi Michael,   Thanks so much for the quick and clear answer! I've ran it on my data. I have two questions (short ones, but with information included): Question 1: When you have the interaction term in the DESeqDataSet (i.e. in the full model), is it correct that this does not allow me to test fo ...
written 22 months ago by Jonas B.0
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TWO-way analysis with DESeq2 - obtaining p-values for the fixed factors and the interaction
... Hi all, I study the effect of cadmium (= a heavy metal) on leaf growth. To give you some background on the experiment: To study the leaf in greater detail, three distinct zones of the leaf are selected: mer, elo and mat (each known for a specific biological process, without bothering now about th ...
deseq2 two-way analysis written 22 months ago by Jonas B.0 • updated 22 months ago by Michael Love25k

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Popular Question 12 months ago, created a question with more than 1,000 views. For Are two biological replicates enough for a transcriptome analysis using DESeq2?

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