## User: ghanbari.msc

ghanbari.msc10
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#### Posts by ghanbari.msc

<prev • 9 results • page 1 of 1 • next >
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... Thanks Michael for the reply.  Just a short question. As you said the following line gives me the difference between treatments at day 21  results(dds, contrast=list(c("DOS21.TreatmentB")), test="Wald") In another post (https://support.bioconductor.org/p/101002/), you suggested that a similar des ...
written 8 months ago by ghanbari.msc10
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... Thanks Michael The last line won't work, because there is no such interaction term DOS8.TreatmentA. Was this a typo?  Yes, it was.  In particular, changing "name" does not recompute p-values for an LRT, unless you add test="Wald". So, you mean if I add test=wald to the code;  res_21_vs_0 = resul ...
written 8 months ago by ghanbari.msc10
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... Thanks for the fast reply. I was wondering if you could also confirm my deseq2 design. I am working on metagenome data which consists of 48 records. My model has two factor: Time and Treatment, having 3-time point: 0, 8,  and 21; Treatment: A (control) and B, so 8 replicates per treatment/time point ...
written 8 months ago by ghanbari.msc10
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... Hi Michael Following your suggestion here is the code that I used.   library("DESeq2") dds.data = phyloseq_to_deseq2(Candela_FEC, ~ DOS + Treatment + Treatment*DOS) dds.data$Treatment <- relevel(dds.data$Treatment, ref="Control") #copy number normalization copy_number_16S = as.matrix(read.tab ...
written 8 months ago by ghanbari.msc10
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... 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 12 months ago by ghanbari.msc10
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... 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 ...
written 12 months ago by ghanbari.msc10 • updated 12 months ago by Michael Love19k
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... 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 12 months ago by ghanbari.msc10
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... 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 ...
written 12 months ago by ghanbari.msc10 • updated 12 months ago by Michael Love19k
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... Fahim, I faced a similar problem. Could you please tell me how did you solve the issue? ...
written 13 months ago by ghanbari.msc10

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