Moderator: b.nota

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b.nota4.6k
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Posts by b.nota

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Answer: A: Differential expression analysis of normalized expression of RNA seq data
... None. There is no package that is able to do (sound) statistical analysis of normalized RNAseq data. Get read count data, and do what you normally do with DEseq2 or limma voom, etc. ...
written 12 hours ago by b.nota4.6k
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Comment: C: Boxplot each row in a dataset in R?
... I know, OP wanted all 4 in one box for each sample... ...
written 1 day ago by b.nota4.6k
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Comment: C: Boxplot each row in a dataset in R?
... This looks more like it, but as you can see only 1 datapoint per entry per sample, so no boxes can be drawn (only a point with its mean the blue bar). ...
written 1 day ago by b.nota4.6k
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Comment: C: Boxplot each row in a dataset in R?
... I agree that you make nice plots, but they are not correct. In OP's example we have 6 samples, each have 4 entries. But in your first example you have 4 samples, some samples have more entries than others... They are mixed up. In your second example You have 4 samples, each seem to have 6 entries of ...
written 1 day ago by b.nota4.6k
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Comment: C: Boxplot each row in a dataset in R?
... Are you sure about this? It seems you divide data of 6 samples over 4 samples now... You plot every "RF.CMSX.posteriorProb" separtely, but each sample has only one value for each, so 4 boxplots wouldn't make sense. I think OP wants one boxplot for all 4: RF.CMS1.posteriorProb-RF.CMS4.posteriorProb ...
written 1 day ago by b.nota4.6k
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Answer: A: Boxplot each row in a dataset in R?
... It depends on how many samples you have, if it will fit in your plot. But lets say you have only 6 samples like in your example, you could get a boxplot like this: boxplot(t(GSE14333_pheno_new[,11:14])) or boxplot(t(GSE14333_pheno_new[1:6,11:14])) ...
written 1 day ago by b.nota4.6k
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Comment: C: Puzzled by GOseq analyses
... Can you provide the code, and plot? I think the failure is the reason why you have a flat line, do you have RNAseq data? ...
written 4 days ago by b.nota4.6k
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Comment: C: Binning GO terms into broader (more usefull) GO terms
... Nice, I hope it can be of help. If you get stuck open a new question here on biostars with the `gogadget` tag. I will try to find a solution. ...
written 4 days ago by b.nota4.6k
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Comment: C: edgeR question from a inexperienced R user
... I am not sure what your understanding of statistics is, but groups with n = 1 are not sound statistics. In the edgeR manual there is even a small section about n = 1 experiments, did you read that? Furthermore, in the same manual, they explain that you need read count data, which you don't have. Co ...
written 4 days ago by b.nota4.6k
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Comment: C: edgeR question from a inexperienced R user
... Hi Janey, I am not sure what your asking, please take more time to explain exactly what you are doing and what the problem is. Maybe you can explain what your experimental design and research question is, or what errors you encounter. I mean I don't even understand what `x` is in your data. Are thi ...
written 5 days ago by b.nota4.6k

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Teacher 21 hours ago, created an answer with at least 3 up-votes. For A: trimming the paired end reads with cutadapt
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