User: cath

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cath30
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2 months ago
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3 months, 2 weeks ago
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c***************@ico.unicancer.fr

Posts by cath

<prev • 10 results • page 1 of 1 • next >
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Comment: C: Gene Density computation in pca.hic
... Thank you very much for you reply. I just understood "density" as a concentration of genes so, to me, it needed to be referenced to the length of the genome "portion" it was computed on. E.g. if there is twice as many bins with score < 0 but same number of genes in bins with score < 0 than in ...
written 9 weeks ago by cath30
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Gene Density computation in pca.hic
... I'm using package HiTC (HiTC_1.22.1) to find A/B compartments in my data. I tried to use gene.gr parameter to directly link eigenvector sign with A/B annotation. However, I got very different results from the ones obtained when trying to compute gene density myself. Looking at pca.hic function, it ...
hitc written 9 weeks ago by cath30
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Comment: C: error with HDF5Array
... I just tried and it works perfectly :-) ...
written 12 weeks ago by cath30
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Comment: C: error with HDF5Array
... Very likely to be the problem. I just tried to change name to paste0(tempdir(), "\\HDF5Array_dump\\auto00001.h5") while debugging H5Fcreate and it worked. Basically, I have: tempdir() [1] "C:\\Users\\CATHER~1\\AppData\\Local\\Temp\\Rtmp02Yt0G" but name [1] "C:\\Users\\Catherine Guérin\\AppData ...
written 12 weeks ago by cath30
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Comment: C: error with HDF5Array
... It's on the same hard drive as where HDF5Array is being installed (location file : "C:/Users/Catherine Guérin/AppData/Local/Temp/Rtmp6nPtSB/HDF5Array_dump/auto00001.h5" ; location of HDF5Array : "C:/Program Files/R/R-3.5.0/library"). There is enough space there (> 52 GB) and I have write permiss ...
written 12 weeks ago by cath30
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Comment: C: error with HDF5Array
... Everything went fine until last lines. I tried with file.choose but I only get the error: HDF5. File accessibilty. Unable to open file. when I pass the last line N.B: I don't know if this is relevant but if I try H5Fcreate("auto00001.h5") outside of library (i.e. directly in the console), it works ...
written 12 weeks ago by cath30
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Comment: C: error with HDF5Array
... @MartinMorgan, I edited the question with both outputs. Thank you ...
written 12 weeks ago by cath30
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Comment: C: error with HDF5Array
... Sorry for the late reply, I didn't get notification of your comment, my installation is indeed valid (or at least biocValid() says so), I'm afraid I won't be able to copy/paste the lines until next tuesday (I'm working at 2 places and I won't be sure to have exact same configuration where I am now) ...
written 3 months ago by cath30
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Comment: C: error with HDF5Array
... I passed the lines above and now I get TRUE for biocValid but for now I still get the error when trying to load HDF5Array. (Previous to passing the lines I had added Rtools to my path). Hopefully it will be solved soon with the different fixes... ...
written 3 months ago by cath30
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error with HDF5Array
... HDF5Array package seems to install correctly but I cannot load it, it gives me the following error: library(HDF5Array) Error : package or namespace load failed for ‘HDF5Array’: .onLoad failed in loadNamespace() for 'HDF5Array', details : call : H5Fcreate(file) error : HDF5. File accessibilty. U ...
biocparallel hdf5array written 3 months ago by cath30 • updated 12 weeks ago by Mike Smith2.8k

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