User: nabiyogesh

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nabiyogesh0
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Posts by nabiyogesh

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Comment: C: Phyloseq to deseq2
... Hi Michael, I am getting data like this for all comparision, but it seems there was some problem: > psfdds <- DESeq(psfdds, test="Wald", fitType="parametric") estimating size factors estimating dispersions gene-wise dispersion estimates mean-dispersion relationship ...
written 5 weeks ago by nabiyogesh0
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Comment: C: Phyloseq to deseq2
... Dear Micheal, thanks a lot, > psfdds<-phyloseq_to_deseq2(ps0, ~1) converting counts to integer mode > psfdds$group <- factor(paste0(psfdds$Tissue,psfdds$Treatment)) > design(psfdds) <- ~ group do I also need to mention Treatment T2 as reference level or I should run further ...
written 5 weeks ago by nabiyogesh0
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Comment: C: Phyloseq to deseq2
... Dear Micheal, you suggesting me to use group for deseq analysis, How I should import data first in deseq2 from phyloseq and then how to run deseq2 if I am just import data without design it says design argument is missing. > psfdds<-phyloseq_to_deseq2(ps0) converting counts to integer mod ...
written 5 weeks ago by nabiyogesh0
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Comment: C: Phyloseq to deseq2
... Hi Michael, I am able to generate plot from deseq2 analysis using below command. But I am not sure whether it is T3_vs_T1 OR T2_vs_T1. could you please suggest how I can improve this analysis more for publication, the aim is to find which microbial species or genus are more abundant in Treat ...
written 5 weeks ago by nabiyogesh0
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Comment: C: Phyloseq to deseq2
... Dear Michael, Thanks for your all help and time. I will run the analysis both way, it will help me to understand deseq2 more. as I mention I have extracted soil samples and want to see the treatment effect T1, T2, T3. I run deseq2 code like this but I am getting some messege: psfdds<-phyl ...
written 5 weeks ago by nabiyogesh0
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Comment: C: Phyloseq to deseq2
... Dear Michael, Thanks for your all help and time. I will run the analysis both way, it will help me to understand deseq2 more. as I mention I have extracted soil samples and want to see the treatment effect T1, T2, T3. I run deseq2 code like this but I am getting some messege: psfdds<-phyl ...
written 5 weeks ago by nabiyogesh0
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Comment: C: Phyloseq to deseq2
... Dear Michael, I read it, but I am much more interested to find treatment (T1, T2 and T3) effect on soil, root and shoot tissue separately so I extract all soil sample, root and shoot in separate files. and now wanted to proceed these file independently so that treatment effect can be analysed on mi ...
written 5 weeks ago by nabiyogesh0
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Comment: C: Phyloseq to deseq2
... Hi Michael , Thanks a lot. From the above data, I have extracted soil samples.I need your help to design the condition for deseq2: here is the summary of data, I have soil sample collection from different villages from two different regions: and we have given three treatment to each soil sample ...
written 5 weeks ago by nabiyogesh0
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Phyloseq to deseq2
... I want to use deseq2 for differential abundance analysis for 16s amplicon data analysis. data detail: I do have three tissue: summary(sample_data(physeq)$Tissue) Leaf Root Soil And each tissue has given 3 treatment. summary(sample_data(physeq)$Treatment) T1 T2 T3 Now I just wa ...
deseq2 written 6 weeks ago by nabiyogesh0 • updated 6 weeks ago by Michael Love23k
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Comment: C: Dendogram from read count to show correlation between biological replicate and s
... Can anyone suggest why I am getting the error in above code? ...
written 22 months ago by nabiyogesh0

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