User: rubi

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rubi90
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Posts by rubi

<prev • 57 results • page 1 of 6 • next >
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Degrees of freedom and coefficients in an edge::deSet and edge::deFit objects
... Hi, Simple question:   How do I see what knots were selected? Anything similar to lm's attr(terms(fit), "predvars")   Thanks   > sessionInfo() R version 3.3.3 (2017-03-06) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: macOS 10.13.6 locale: [1] en_US.UTF-8/en_US.UTF-8/en_ ...
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Assessing goodness of fit of a limma model fitted to microarray data
... Hi,   I have gene expression data from two species, where both were treated similarly at time = 0 and RNA was purified at time points 0 (i.e., before treatment), 0.5, 1, 2, 3, 4, 6, 8, 10, 12, 18, 24, 48, 72, and 168 hours. For both species, there are 4 biological replicates per each time > 0, ...
microarray limma goodness of fit written 3 months ago by rubi90
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Comment: C: Design matrix for a two-color experimental design testing for time effect on 3 t
... Thanks again @Gordon Smyth. The reason for the error is the GAL annotation file. It has a few non-probe rows in it, e.g.: Block Column Row Name ID RefNumber ControlType GeneName TopHit Description 1 1 1 1 GE_BrightCorner GE_BrightCorner ...
written 3 months ago by rubi90
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Comment: C: Design matrix for a two-color experimental design testing for time effect on 3 t
... Sure. Just added it at the bottom of my post.   Thanks a lot. ...
written 3 months ago by rubi90
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Comment: C: Design matrix for a two-color experimental design testing for time effect on 3 t
... Thanks a lot for answer @Gordon Smyth. I edited my question to make it clearer and address your questions, but let me also reply here. My biological question is which genes show time-dependent changes in expression due to irradiation (i.e., which genes go up and down with time due to the irradiati ...
written 3 months ago by rubi90
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Design matrix for a two-color experimental design testing for time effect on 3 treated cell-lines, each with its own time=0 control
... Hi, I did microarray gene-expression profiling on the following experimental design: I took three cell lines and plated each one of them in four plates, hence a total of 12 plates. I purified RNA from a single plate of each of the three cell lines at time=0, then X-ray irradiated the remaining pl ...
microarray twochannel limma design matrix written 3 months ago by rubi90 • updated 3 months ago by Gordon Smyth35k
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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 6 months 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 6 months ago by rubi90 • updated 6 months ago by Mike Smith3.1k
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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 6 months 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 7 months ago by rubi90 • updated 7 months ago by Aaron Lun21k

Latest awards to rubi

Popular Question 3 months ago, created a question with more than 1,000 views. For Rsubread featureCounts with strand information
Popular Question 6 months ago, created a question with more than 1,000 views. For Filtering lowly expressed genes in voom-limma analysis
Supporter 21 months ago, voted at least 25 times.

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