User: hsbio

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hsbio10
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Posts by hsbio

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Comment: C: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
... Thanks. This seems to get rid of the majority of those cases. Just to confirm, if I then still apply lfcShrink with apeglm, using those shrunken log fold changes with the adjusted p values (from results(dds), rather than the calculated s values) is still reasonable for things like visualization/r ...
written 20 days ago by hsbio10
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Comment: C: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
... Thanks for your response Looking into this more, I noticed that actually no genes are being filtered as outliers (i.e. based on cooksCutoff) and then I realised that this is due to my design (or at least I think it is). So essentially, my samples are from 3 different tissues which are sometimes fro ...
written 20 days ago by hsbio10
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Comment: C: Normalizing counts using TIN metric before DESeq2
... Hi Michael, Many thanks for the response. I have never used RUV or SVA before but I will have a read of those and try them here and will post if I have any further questions. Thanks again. ...
written 21 days ago by hsbio10
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DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
... Hello, I've done some differential expression analysis with 3 main groups (3 or 4 biological replicates for each group, 11 total samples). When comparing any two of the groups, there are a number of genes that are statistically significant (in some cases, quite a lot) that have very high log2FoldCh ...
deseq2 written 21 days ago by hsbio10
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Normalizing counts using TIN metric before DESeq2
... Hi, I have some total RNA-seq data that was obtained from RNA that had quite low RIN values (unfortunately due to the source material, this was pretty much unavoidable). I've been looking at different ways people have tried to approach this problem and try and correct for it. I've seen that the tra ...
deseq2 salmon tximport written 4 weeks ago by hsbio10 • updated 4 weeks ago by Michael Love25k
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Comment: C: deseq2 analysis with multiple factors and interaction terms
... Hi, Thanks for that suggestion.  I've done that and would just like to confirm a few things. In this design: results(dds,name="genotypeA.treatmenttreated1hr") would essentially be the treatment effect at 1 hr in genotype A or (treatment at 1 hr vs control treatment in samples that are genotype A) ...
written 23 months ago by hsbio10
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Comment: C: deseq2 analysis with multiple factors and interaction terms
... Hi Micheal,  Thanks for the response. I think that would be one way I would want to look at it. Would it also be a possibility to say look at whether the differences over time, say 1hr vs 30 min are different over genotypes. Perhaps this would over-complicate it a bit.  And yes, some of the combin ...
written 23 months ago by hsbio10
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deseq2 analysis with multiple factors and interaction terms
... Hi, I am trying to do some differential expression analysis with deseq2 at the moment and I have samples with 3 different groups; genotype (A and B), treatment (control and treated), time (1hr vs 30). Each set of conditions has at least 3 replicates. I have tried to have a read through previous thr ...
deseq2 differential gene expression multiple factor design differential analysis written 23 months ago by hsbio10 • updated 23 months ago by Michael Love25k

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Popular Question 22 months ago, created a question with more than 1,000 views. For deseq2 analysis with multiple factors and interaction terms

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