User: Giovanni Bacci

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Italy, Florence, University of Florence
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Posts by Giovanni Bacci

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Comment: C: Deviance decomposition with DESeq2
... Dear Michael, thanks for your help! I changed my code as follows: # Full model dds.full <- DESeq(dds.full, test = "Wald", fitType = "parametric", betaPrior = T) # Deviance estimation of reduced models deviances <- sapply(models[-1], function(m){ dds <- dds.full # Copying the full model ...
written 8 weeks ago by Giovanni Bacci0
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Comment: C: Deviance decomposition with DESeq2
... Sorry if I come back to this after quite a long time, but I'm still struggling to produce reliable results. It seems that the above calculation produced some negative values. I would say that the factor considered is somehow worsening the model by increasing the deviance of the full model in respect ...
written 8 weeks ago by Giovanni Bacci0
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Deviance decomposition with DESeq2
... Hello, I'm using DESeq2 to analyse a large dataset with basically three predictors: 1 - Subjects = the ID of the subject involved in the experiment (categorical) 2 - Culture medium = the culture medium (categorical) 3 - Time = the number of days (continuous) I would like to inspect the proporti ...
deseq2 analysis of deviance written 4 months ago by Giovanni Bacci0 • updated 4 months ago by Michael Love19k
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Comment: C: DESeq2 multifactor design with interaction term
... Hi Mark and thank again for your help! If I understood correctly the interaction between, let's say, food B and subject 5002 should be: (5002.B - 5002.A) - (5001.B - 5001.A) if that holds, the interaction between food B and subject 5003 should be: (5003.B - 5003.A) - (5001.B - 5001.A) so if I ...
written 5 months ago by Giovanni Bacci0
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Comment: C: DESeq2 multifactor design with interaction term
... That was my fault! I was giving the unfiltered table to my plotting function, sorry. The function now works well and the zero-counts OTUs have been removed. My last question regarding the interaction part of the original post: If I understood correctly I can extract contrasts between food B and C ...
written 5 months ago by Giovanni Bacci0
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Comment: C: DESeq2 multifactor design with interaction term
... Let me clarify that: the function lfcShrink worked fine with both methods but the output still contains zero-count OTUs. The worst thing is that they have a huge log2FoldChange and a very small p-value so it is really difficult to remove them in a "programatic" way without removing valid difference ...
written 5 months ago by Giovanni Bacci0
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Comment: C: DESeq2 multifactor design with interaction term
... I tried with lfcShrink (both with apeglm and ashr) and it doesn't seem to work. As you said I actually have 16S rRNA data they are not RNA-seq and they could not follow negative binomial distribution (I tried to model them with glmmADMB and in some cases the Poisson family seems to work better than ...
written 5 months ago by Giovanni Bacci0
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Comment: C: DESeq2 multifactor design with interaction term
... Thanks for the reply! Sorry to bother you but I'm trying to fully understand how DESeq2 builds result tables. The steps I reported for subject2 can be considered correct? I was planning to use DESeq2 for other studies where I cannot make the simplification that you suggested so I need to know if (i ...
written 5 months ago by Giovanni Bacci0
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DESeq2 multifactor design with interaction term
... Hello, I'm running DESeq2 in combination with phyloseq to analyze 16S rRNA data coming from a large survey. I have gut microbiome coming from 6 subjects (called 5001, 5002, 5003, 5004, 5005, and 5006) that experimented 3 types of diets (called A, B, and C). I would like to test differences between: ...
deseq2 multiple factor design interaction term written 5 months ago by Giovanni Bacci0 • updated 5 months ago by Michael Love19k

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