User: reubenmcgregor88

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Posts by reubenmcgregor88

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Comment: C: pcaEcplorer PCA2go function crashing
... Update: The airways data works fine with PCA2go?   ...
written 3 months ago by reubenmcgregor880
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Comment: C: pcaEcplorer PCA2go function crashing
... Ah I see, Done, thanks. I will run the airway set tomorrow. ...
written 3 months ago by reubenmcgregor880
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Comment: C: pcaEcplorer PCA2go function crashing
... I am happy to provide the data to see if you can replicate the issue, It is only a subset of the data anyway (I am carrying out the analysis on a subset of genes). Shall I email it to you? If so which email shall I use? In the meantime I can try the airway data. Thank you again, Reuben ...
written 3 months ago by reubenmcgregor880
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Answer: A: pcaEcplorer PCA2go function crashing
...     Hi Federico, thank you fro replying, I am using output from DESeq2 on human samples, with gene symbols. There are 6 samples in total, with 2 condition (eth and vitd) and looks something like this when I print normalised counts: > normcounts <- counts(ddsMF, normalized = TRUE) > View ...
written 3 months ago by reubenmcgregor880
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pcaEcplorer PCA2go function crashing
... Hi, I am trying to run pacExplorer on Deseq2 results. Gret programme and everything works fine until I try and use the PCA2GO function, I get the following error: Warning: Error in [: subscript out of bounds Stack trace (innermost first):     95: limmaquickpca2go     94: eval     93: eval     92: ...
pcaexplorer pca2go written 3 months ago by reubenmcgregor880 • updated 12 weeks ago by Federico Marini90
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Answer: A: Error in pcaplot3d from pcaExplorer, when running Deseq2 since update of package
... UPDATE: For anyone having the same issue, it was the "threejs" package update that was messing with the output! I installed the older version: > require(devtools) > install_version("threejs", version = "0.2.2", repos = "http://cran.us.r-project.org") And then plot3dpca runs fine again, I ...
written 3 months ago by reubenmcgregor880
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Error in pcaplot3d from pcaExplorer, when running Deseq2 since update of packages
... Hi,  I was plotting 3D PCA's from Desq2 output using simple: > pcaplot3d(ddsMF, intgroup = "donor") I then updated some packages: > install.packages(c("httr", "Matrix", "plotrix", "shape", "shiny", "threejs", "tidyr")) And now the pcaplot3D function returns this error: Error in scatterpl ...
deseq2 pcaexplorer written 3 months ago by reubenmcgregor880
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Comment: C: DESeq2 multifactorialdesign contrasts
... Thank you Gavin, I see your points, both of them. I am using the most recent DESeq2 version, sorry I should have specified version etc.  However, as far as I can gather, there is something wrong with my design, please bare with me. when I run the original: > dds <- DESeqDataSetFromMatrix(c ...
written 3 months ago by reubenmcgregor880
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DESeq2 multifactorialdesign contrasts
...   Hi all,  I have what may seem like as really simple questions, but being new to using R in general and very new to DEseq2 I just can not figure it out reading the manual (which is great and very informative for a biologist, thanks!) I have a simple design of 3 donors (A, B and C) and 3 conditio ...
rnaseq deseq2 design and contrast matrix multifactorial design written 3 months ago by reubenmcgregor880 • updated 3 months ago by Gavin Kelly510

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