User: ghanbari.msc

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ghanbari.msc10
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Posts by ghanbari.msc

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Comment: C: DESeq2 on 16S copy number corrected genes
... 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 11 months ago by ghanbari.msc10
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Comment: C: DESeq2 on 16S copy number corrected genes
... 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 11 months ago by ghanbari.msc10
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Comment: C: DESeq2 on 16S copy number corrected genes
... 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 11 months ago by ghanbari.msc10
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Comment: C: DESeq2 on 16S copy number corrected genes
... 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 11 months ago by ghanbari.msc10
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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 14 months 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 14 months ago by ghanbari.msc10 • updated 14 months ago by Michael Love20k
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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 15 months 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 15 months ago by ghanbari.msc10 • updated 15 months ago by Michael Love20k
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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 16 months ago by ghanbari.msc10

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