User: Andy91

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Andy9130
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Posts by Andy91

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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 26 days 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 26 days 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 27 days 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 27 days 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 27 days 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 27 days 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 27 days ago by Andy9130
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Downloading Twochannel microarray data from ArrayExpress
... Dear Bioconductor, I am currently in the process of performing a study on various microarray datasets, some of which are two channel microarrays. For consistency reasons, I would like to download the raw two channel data. As such I resorted to the “ArrayExpress” R package. I have experienced quite ...
microarray twochannel arrayexpress written 28 days ago by Andy9130
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Meta Analysis on CAMERA results
... Dear all, I would like to perform a meta analysis on the gene sets that I observed using CAMERA. Has anybody had experience with comparing gene sets between studies that performed the same experiment? Would it make sense to extract the t-statistic from CAMERA and use that to calculate the Cohen d a ...
limma camera meta analysis cohen d written 9 months ago by Andy9130
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Answer: A: UcscTrack and BED without headers
... Thanks for the great work! ...
written 22 months ago by Andy9130

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