User: akp

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akp0
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Posts by akp

<prev • 10 results • page 1 of 1 • next >
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Comment: C: installation failed when trying msa
... Thanks, no worries; I look forward to hearing from you :-) ...
written 2.5 years ago by akp0
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installation failed when trying msa
... I am trying to install "MSA" as, source("https://bioconductor.org/biocLite.R") biocLite("msa") - but I fece the following erorrs, g++: error: ./libgc.a: No such file or directory g++: error: ./libClustalW.a: No such file or directory g++: error: ./libClustalOmega.a: No such file or directory g ...
msa written 2.5 years ago by akp0 • updated 2.5 years ago by UBodenhofer250
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Answer: A: DESeq2 blocking by condition over time
... I think, I haven't explained myself well, let me try one more time. Bacterial abundance of three different groups across 10 weeks is measure. Therefore, I chose this formulation/design to answer what are the taxa( in RNA world genes) that are distinguishing these three groups over the time. diagdds ...
written 2.5 years ago by akp0
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DESeq2 blocking by condition over time
... I am using deseq2 to find differential significant taxa (count data). The data is longitudinal and three groups of mice and I am using sth like diagdds = phyloseq_to_deseq2(physeq.fecal, ~ condition + week_experiment +                              team + condition:week_experiment) since I have th ...
phyloseq deseq2 time course written 2.5 years ago by akp0
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Comment: C: DESEQ2 blocking design doesn't match expectation !
... Thanks, in fact it looks more reasonable - but are you sure, the contract should be like that but not the other way around ? ((I have updated my code with the contrast thing)) ...
written 2.7 years ago by akp0
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Comment: C: DESEQ2 blocking design doesn't match expectation !
... Does it look better ? ...
written 2.7 years ago by akp0
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DESEQ2 blocking design doesn't match expectation !
... I would like to estimate DE between a gene in a case and control, however, there are two underlying teams (A and B) (the experiment was run in two batches) so I would like to consider them as well.  the data format is sth like below and I have made sure, "condition" and "team" are factor ...
deseq2 block pca written 2.7 years ago by akp0
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Comment: C: deseq2 normalized data
... I am going to use a predictive model, to classify cancer / non-cancer. You can think, of it as a logistic regression; and eventually, my models returns some coefficient for every covariates(genes); Then if a new data comes, based on those coefficients I can assign new data points into either classes ...
written 3.5 years ago by akp0
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Comment: C: deseq2 normalized data
... regressing genes on the outcome ( case/control ).   ...
written 3.5 years ago by akp0
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deseq2 normalized data
... I understand the idea of using negative bionomial distribution to test whether a covariate is differentially expressed/abundant or not. I wonder, if the same argument is valid, when the analysis is not performing any test but for example, regressing these genes over case/control. In this regression ...
regression deseq2 counts written 3.5 years ago by akp0 • updated 3.5 years ago by Michael Love22k

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