User: ghanbari.msc

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ghanbari.msc10
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Posts by ghanbari.msc

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Comment: C: problem with DESeq2 on metagenome analysis
... Thanks Michael for a fast reply. So in case that the within variability is not that much different among gut sections, my current design is ok, right?  dds$group <- factor(paste0(dds$gutsection, dds$treatment)) design(dds) <- ~ group dds <- DESeq(dds) resultsNames(dds) results(dds, contra ...
written 8 weeks ago by ghanbari.msc10
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problem with DESeq2 on metagenome analysis
... Hello,  I have metagenome samples from 24 animals. and for each animal, the samples were taken from three different locations (Ileum, Caecum and Colon). I tested the effect of three treatments (8 animals/treatment) on the metagenome level and Now I want to use DESeq2 tool to find the specific genes ...
deseq2 metagenome written 8 weeks ago by ghanbari.msc10 • updated 8 weeks ago by Michael Love15k
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Comment: C: DESeq2 on 16S copy number corrected genes
... Thanks Michael for the reply. I have the number of 16S copy per sample but I do not know how to create a matrix out of it. The data are like this:                     Sample1 Sample2    Sample3 ...... 16S copy      2000         1500         1000     ...... Do you have a suggestion on how to creat ...
written 11 weeks ago by ghanbari.msc10
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DESeq2 on 16S copy number corrected genes
... Hi  I am currently working on some metagenome data and I'd like to use DESeq2 tool to find the genes that are differentially abundant in different treatment over time. Due to the type of the study, I need to normalize the count data (genes abundance) per 16S rRNA copy number which changes the distr ...
metagenomics deseq2 written 11 weeks ago by ghanbari.msc10 • updated 11 weeks ago by Michael Love15k
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Comment: C: DESeq2 - Error in estimateSizeFactorsForMatrix(counts(object)
... Fahim, I faced a similar problem. Could you please tell me how did you solve the issue? ...
written 3 months ago by ghanbari.msc10

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