User: adesrichard

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Posts by adesrichard

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Comment: C: BiocParallel/scater warning after move to R 3.4.0
... Hi Martin! You are correct. fgsea loads but I can't use it unless I use serial parameters, not multicore. Here is what I am getting when trying to register : > library(BiocParallel) > register(MulticoreParam()) Error in validObject(.Object) : invalid class “MulticoreParam” object: 1: ‘c ...
written 2.1 years ago by adesrichard0
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Comment: C: BiocParallel/scater warning after move to R 3.4.0
... I had the exact same issue today, I cannot run fgsea package anymore.  > library("fgsea", lib.loc="/usr/local/lib/R/site-library") Loading required package: Rcpp 'BiocParallel' did not register default BiocParallelParams: invalid class “MulticoreParam” object: 1: ‘cluster’, ‘.clusterargs’, ‘. ...
written 2.1 years ago by adesrichard0
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Answer: A: DESEq2 Paired samples Before and after treatment
... That makes sense indeed!  Thank you very much guys, this solved my problems and answered my questions. Thank you for your support! Alex ...
written 2.9 years ago by adesrichard0
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Answer: A: DESEq2 Paired samples Before and after treatment
... Thank you very much for all the help Michael! After following your instructions, I first tested the design which worked well. ~Response+ Response:Patient.n + Response:Treatment However, when I add status to the design, I have model that is not full ranked again. I tried to add a nested Status co ...
written 2.9 years ago by adesrichard0
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Comment: C: DESEq2 Paired samples Before and after treatment
... Thank you very much Michael for the guidance! Does this means that patient 5 will be eliminated from the response analysis? In this case, isn't the choice of which patient is being excluded/included in the analysis be considered? If yes, let's say I have 100 patients instead, keeping the same propo ...
written 2.9 years ago by adesrichard0
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Comment: C: DESEq2 Paired samples Before and after treatment
... Hi Mike, I read the instruction about the interaction term and nested individuals but I am still unclear what design I should use and what parameters to input in the `DESeq()` function. This is mainly because the number of responders and non-responders is different in my design, which is not the ca ...
written 2.9 years ago by adesrichard0
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Comment: C: DESEq2 Paired samples Before and after treatment
... Hello Michael,  Thank you for your comment! I am running DESeq2 version 1.12.3. The complete error I am getting is as followed : using pre-existing size factors estimating dispersions gene-wise dispersion estimates Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so the ...
written 2.9 years ago by adesrichard0
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Answer: A: DESEq2 Paired samples Before and after treatment
... Hi Simon,   Thank you very much for your quick reply! I tried to follow you instructions and had no problem with the following design: ~ Patient.ID + Treatment However, for the two other design, it seems like my model matrix is not full rank and DESEq give me the following error. df=data.fra ...
written 2.9 years ago by adesrichard0
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Comment: C: DESEq2 Paired samples Before and after treatment
... Hi Simon, I modified the code to make up for the  mistake you caught up. Thanks a lot! ...
written 2.9 years ago by adesrichard0
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DESEq2 Paired samples Before and after treatment
... Hi everyone, I would like to use DESeq2 to process RNASeq paired samples (before and on treatment). I read very carefully the different posts and tutorial but I am still uncertain on how to design my experiment formula. Here are my experimental factors : df=data.frame(Patient.ID = factor(rep(1:8, ...
deseq2 paired samples written 2.9 years ago by adesrichard0

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