## User: nhua

nhua0
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#### Posts by nhua

<prev • 11 results • page 1 of 2 • next >
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... Hello, I wanted to ask if using the following model design was appropriate for the question I'm trying to answer. I have samples that are paired (BG and AG status). The samples come from 8 individuals and each individual has a BG and AG sample. Additionally, there are 4 treatment groups (A, C, T, E ...
written 16 months ago by nhua0
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Comment: C: Paired Difference Analysis
... Good afternoon Dr. Love, I tried my hand at using Limma, then metagenomeSeq since the fitZig function also allows for duplicate correlation. However, I had a few issues with using that package, so I decided to only include samples found in all of the treatments. However, when I pruned the samples f ...
written 19 months ago by nhua0
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Comment: C: Paired Difference Analysis
... Hello,  I wanted to see what the results would be comparing the design that you posted to the results outputted by the group design. They’re the same values, but the log2FoldChange and stat columns are of the opposite signs. I think it’s because the grouping design compares “Crafter vs Crbefore“ wh ...
written 20 months ago by nhua0
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Comment: C: Paired Difference Analysis
... Also clarifying an earlier question, is there a need to filter out samples to control for the the donors? I would think so because the gene expression should be compared between the same individuals. So, if Treatment Aq had 10 donors and Treatment Cr had 20 donors, and they only shared 10 of the sam ...
written 21 months ago by nhua0
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Comment: A: Paired Difference Analysis
... Thanks!  Also clarifying an earlier question, is there a need to filter out samples to control for the donors? I would think so because the gene expression should be compared between the same individuals. So, if Treatment Aq had 10 donors and Treatment Cr had 20 donors, and they only shared 10 of t ...
written 21 months ago by nhua0
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Comment: C: Paired Difference Analysis
... Another question. Earlier, I created this design using grouping:  dd_tb <- phyloseq_to_deseq2(paired_joined_ps, design = ~ Status + Treatment) dd_tb$group <- factor(paste0(dd_tb$Treatment, dd_tb\$Status)) design(dd_tb) <- ~ group   Do the results from this design match the results from: ...
written 21 months ago by nhua0
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Comment: C: Paired Difference Analysis
... Referring to the DESeq2 vignette, for gene 2, using the “genotype:condition” interaction term means that the results function should return the difference between the condition effect of genotype II and condition effect for genotype III. And condition effect refers to the difference between conditio ...
written 21 months ago by nhua0
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Comment: C: Paired Difference Analysis
... I see, but is there a way we could contrast (TreatmentCr.StatusBG, TreatmentCr.StatusAG) to (TreatmentAq.StatusBG, TreatmentAq.StatusAG)? I guess a difference of differences would be a more fitting analysis.  ...
written 21 months ago by nhua0
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Comment: C: Paired Difference Analysis
... Hi Michael, The previous table laid out the different number of samples I had per treatment. They all varied because certain samples weren’t able to get sequenced. If I were to compare the difference of statuses (BG and AG) between the samples of treatments A and C, would I be able to since treatme ...
written 21 months ago by nhua0
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Comment: C: Paired Difference Analysis
... Hi Michael, These are the total samples we have per treatment. It probably doesn't help that not all of the same samples are found across all of the treatments. All of the treatments contain the same 8 samples, so would we only be able to include those samples in the analysis? The null hypothesis i ...
written 22 months ago by nhua0

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