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... 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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... 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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... 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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... 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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... 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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... 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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... 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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... 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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... 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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... 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, ...
written 2.9 years ago by adesrichard0