User: Andy91

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Andy9130
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Posts by Andy91

<prev • 17 results • page 1 of 2 • next >
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Comment: C: edgeR trended or tagwise
... I see, thank you for the answer. So even if the NB dispersion is known, you should not use tagwise dispersion for glmQLFit. In which situation would you use tagwise dispersion? Or is it simply a diagnostic measure. ...
written 2 days ago by Andy9130
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Comment: C: edgeR trended or tagwise
... I see, I guess my understanding of the BH method is currently lacking, I'll read more into that. Thank you for the answer ...
written 5 days ago by Andy9130
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edgeR trended or tagwise
... Dear Bioconductor, I am currently performing an RNAseq analysis on rat samples using edgeR. Data was aligned using STAR against the rat genome (Rnor v6.0) and the genes were counted using featureCounts against the Ensembl Rnor gtf file. The experimental design comprises two factors: DSS and stimul ...
edger glmqlftest() written 5 days ago by Andy9130 • updated 5 days ago by Aaron Lun18k
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Comment: C: Error using read.metharray.exp in minfi to read idat files
... Hi Kasper, I think at this point there is not much extra you could do, in the manual the entry for read.meth.exp states that the base argument represents the base directory, at most you could perhaps make a note that this represents the full/relative from the working directory path to the directory ...
written 11 weeks ago by Andy9130
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Answer: A: Receiving error trying to import matrix into DESeq2
... I cannot say anything about your count matrix as you would have to provide an example of it (i.e. head(countData)). The error seems to suggest that your provided design matrix ("colData") is not well designed. If the provided example is what you are using, the issue would be that the "Age" object c ...
written 12 weeks ago by Andy9130
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Comment: C: Error using read.metharray.exp in minfi to read idat files
... So I was able to reproduce your error using the minfiData on Bioconductor. The "Basename" column in your samplesheet should contain the full/relative path to the IDAT files, i.e. "/home/poojitha/idats/5684819001_R01C01". The easiest way out IMO is to use the function read.metharray.sheet([base_dire ...
written 12 weeks ago by Andy9130
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Comment: C: Error using read.metharray.exp in minfi to read idat files
... Could you show the directory structure of the location where all your .idat files are located? Are they located in subfolders, or are they all located in the same folder? How does your samplesheet look like? ...
written 12 weeks ago by Andy9130
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Comment: C: PCA plot for TPM data
... I would recommend you do some reading on plotting in R. Example tutorials: http://www.cyclismo.org/tutorial/R/plotting.html http://www.cyclismo.org/tutorial/R/intermediatePlotting.html http://tutorials.iq.harvard.edu/R/Rgraphics/Rgraphics.html   Pertaining the question at hand, you could us ...
written 12 weeks ago by Andy9130
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Answer: A: PCA plot for TPM data
... You can do it with base R. One way of doing it is first transposing the TPM count matrix (assuming you want to run PCA on the samples rather than the genes), centering it, then doing an SVD and subsequently plotting the first and second columns of the u matrix (assuming you are interested in the fir ...
written 12 weeks ago by Andy9130
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Answer: A: Error using read.metharray.exp in minfi to read idat files
... One oddity I observe in your output is that the zeros of the plate position have been replaced with an "O". This does not appear to be the case for the plate IDs. ...
written 12 weeks ago by Andy9130

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