User: rubi

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rubi90
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Posts by rubi

<prev • 51 results • page 1 of 6 • next >
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Comment: C: Low level usage of rhdf5
... Thanks a lot.   It's also failing with these type combinations: h5.space <- rhdf5::H5Screate(type="H5S_SIMPLE") h5.dataset <- rhdf5::H5Dcreate(h5loc=bottom.group,name="val",dtype_id="H5T_STD_I32LE",h5space=h5.space)   h5.space <- rhdf5::H5Screate(type="H5S_SIMPLE") h5.dataset <- ...
written 8 weeks ago by rubi90
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Low level usage of rhdf5
... I'm trying to create an hdf5 file using R's rhdf5 package. I want to create this group hierarchy: "top/bottom". In "bottom", I'd like to have two datasets (both H5S_SCALARs): "score" which is an "H5T_IEEE_F64LE" type "type" which is an "H5T_STRING" type I thought this would work:   output. ...
rhdf5 written 8 weeks ago by rubi90 • updated 8 weeks ago by Mike Smith2.7k
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Create a soft link in rhdf5
... Hi, I'm trying to create an hdf5 structure with softlinks that point to other parts of the hdf5 structure. For example, I want description to be a softlink pointing to a clustering/_kmeans_9_clusters/description group in my hdf5 structure so that I'll see: SOFTLINK "description" { ...
rhdf5 softlink written 8 weeks ago by rubi90
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Using HDF5Array writeHDF5Array for a large dgCMatrix
... Hi, I have a large sparse matrix (40,000 by 40,000, called mat) as a dgCMatrix which I would like to save to an HDF5 file. The conversion of the dgCMatrix to an array (arr <- as(Matrix::as.matrix(mat),"HDF5Array")) is very slow and then writing the array to the HDF5 file, using:  writeHDF5Array ...
hdf5array dgcmatrix written 12 weeks ago by rubi90 • updated 12 weeks ago by Aaron Lun19k
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Answer: A: getGEO error when trying to download a series matrix file
... Thanks a lot ...
written 3 months ago by rubi90
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Comment: C: Does fgsea order the stats argument?
... Yep, that's exactly what I'm doing. ...
written 3 months ago by rubi90
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getGEO error when trying to download a series matrix file
... Hi, I'm trying to use GEOquery's getGEO for downloading the series matrix file of several studies using their GEO accessions, from my linux cluster. I originally tried: geo.accession <- "GSE11675" out.dir <- "~/Downloads/GSE11675" GEOquery::getGEO(GEO = geo.accession, GSEMatrix = T, AnnotG ...
geoquery getgeo written 3 months ago by rubi90
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Comment: C: Does fgsea order the stats argument?
... Sorry for the late response. I'm using a Bayesian differential expression tool (MMDIFF), which provides an estimate of the effect size (e.g. ln(fold-change) between treatment and control), the posterior probability that the estimated effect size is different from 0. Unlike the frequentist approaches ...
written 3 months ago by rubi90
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Comment: C: Getting error using GenomicRanges::setdiff
... Right, sorry about that and thanks a lot for the help. ...
written 10 months ago by rubi90
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Comment: C: Getting error using GenomicRanges::setdiff
... Thanks a lot.   This, however, returns also the introns. Is it possible to get only the UTRs or to systematically remove the introns? ...
written 10 months ago by rubi90

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Supporter 16 months ago, voted at least 25 times.

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