User: nabiyogesh

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Posts by nabiyogesh

<prev • 38 results • page 1 of 4 • next >
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Comment: C: deseq2 formula design
... Dear Michael, Thanks, please help me to understand it. Deseq2 vignette says it can be because of two reasons, but I did not able understand it but I think certainly these two factors are not linear combination. “the model matrix is not full rank, so the model cannot be fit as specified.” There ar ...
written 4 weeks ago by nabiyogesh0
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taxonomy download from NCBI based on geneID
... Is it possible to download taxonomy based on gene Id for a large dataset from NCBI using biomartr package? vi arsM.ID.txt AAAK03000116.1 AAAL02000001.1 AACD01000079.1 AACS02000002.1 AADV02000002.1 AADV02000014.1 AADV02000142.1 AADV02000157.1 AADV02000160.1 A ...
biomartr bioconducter written 4 weeks ago by nabiyogesh0
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deseq2 formula design
... Hi, I do have samples collected from 2 different region and from each region we collected sample from 9 villages like this Rajshahi ----9 villages Mymensingh --9 villages Now I want to do differential microbial abundance between Rajshahi and Mymensingh, but by controlling for the effect of villag ...
deseq2 written 4 weeks ago by nabiyogesh0 • updated 4 weeks ago by swbarnes2240
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Comment: C: vegdist for beta diversity
... thanks, it is resolved, I just need to transpose the count data. ...
written 5 weeks ago by nabiyogesh0
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vegdist for beta diversity
... Hi, I am trying to use vegan bioconducter package for beta diversity and permutation analysis for amplicon data but it is giving distance according to ASV instead of sample names, please help me with it. > werra_sp <- read.table("convent.fert.root.count.txt",header=T,sep='\t', ...
vegan written 5 weeks ago by nabiyogesh0
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Comment: C: Phyloseq to metagenomeSeq
... thanks Hector for your all help. obj <- MRcounts(obj, norm = TRUE, log = TRUE). do you also suggest while running MetagenomeSeq should I also use MRcount for normalisation instead of these three line R code: obj = cumNorm(obj, p = cumNormStatFast(obj)) normFactor = normFactors(obj) ...
written 10 weeks ago by nabiyogesh0
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Comment: C: Phyloseq to metagenomeSeq
... Dear Hector, Thanks for your response, I also want to compare abundant ASV from metagenomeSeq with normalized ASV count, for that should I use output from below command, will it give me normalized ASV count? and then I want to convert it into log2 value and can cross check the metagenomeSeq resul ...
written 10 weeks ago by nabiyogesh0
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Comment: C: phyloseq to edgeR
... Thanks a lot Smyth. I just want to add one more thing that these treatment were collected from 9 different locations so to ignore the location effect do I need to change group formula to location + Treatment? location is also a part of metadata column as like treatment. and then can I use the the ...
written 10 weeks ago by nabiyogesh0
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phyloseq to edgeR
... Hi, I do have three treatment condition (T1, T2 and T3), could you please suggest how I can improve below code to extract pairwise comparisons in edgeR after importing data from phyloseq object to edgeR. dge = phyloseq_to_edgeR(kosticB, group="Treatment") # Perform binary test et = ex ...
edger written 11 weeks ago by nabiyogesh0 • updated 11 weeks ago by Gordon Smyth38k
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Comment: C: Phyloseq to metagenomeSeq
... Thanks Hector, do you mean I should use this command like below: settings = zigControl() thanks for your time and help. nabiyogesh ...
written 11 weeks ago by nabiyogesh0

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