User: Diego Diez

gravatar for Diego Diez
Diego Diez700
Reputation:
700
Status:
Trusted
Location:
Japan
Website:
http://qimm.ifrec.osak...
Scholar ID:
Google Scholar Page
Last seen:
1 day, 5 hours ago
Joined:
13 years, 5 months ago
Email:
d**********@gmail.com

I am a researcher at the Immunology Frontier Research Center, Osaka University. My background is biochemistry and bioinformatics. I am interested in complex systems and understanding how living organisms are organized and respond to external stimuli. My research focuses on the understanding of immune system's alterations in complex diseases.

Posts by Diego Diez

<prev • 158 results • page 1 of 16 • next >
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Comment: C: Error with BiomartGeneRegionTrack: could not find symbol "recursive"
... This is fixed following https://support.bioconductor.org/p/93347/#93373 (setting type = "source" and installing GenomicRanges). ...
written 8 months ago by Diego Diez700
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Comment: C: Combining RangedData objects is broken (IRanges 2.8.1 with R version 3.3.3 RC)
... Great, works for me but had to specify type = "source" in order to fix the problem. ...
written 8 months ago by Diego Diez700
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Error with BiomartGeneRegionTrack: could not find symbol "recursive"
... Since updating to R-3.3.3 yesterday (not clear if related) I get the following error when using BiomartGeneRegionTrack: library(Gviz) BiomartGeneRegionTrack(symbol = "Stat1", genome = "mm9") Error in .Primitive("c")() : could not find symbol "recursive" in environment of the generic function ...
gviz written 8 months ago by Diego Diez700
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consensusString fails for AAMultipleAlignment object
... I get the error: Error in cmat[codes, , drop = FALSE] : subscript out of bounds It seems consensusString calls consensusMatrix, which returns the letter probabilities for the standard amino acids: rownames(consensusMatrix(aln)) [1] "-" "A" "C" "D" "E" "F" "G" "H" "I" "K" "L" "M" "N" "P" "Q" "R" ...
biostrings written 12 months ago by Diego Diez700
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Comment: C: Why the log fold change of some genes returned by edgeR is not compatible with t
... The first thing that comes to my mind is that you should probably include the code you used to obtain these values. And the output of sessionInfo(). ...
written 13 months ago by Diego Diez700
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Answer: A: surrogate variable analysis using R package "sva"
... `sva()` returns a list with several components. One is `sv` which contains the surrogate variables. You can include those variables  in your model (with *limma/edgeR/DEseq2*). Take a look at `?sva` and the vignette (calling `browseVignettes("sva")` in R) for more details, limitations and examples on ...
written 13 months ago by Diego Diez700
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Comment: C: Comparison of Column of AnnotatedDataFrame
... I see! I completely forgot I used the slot to access the data for checking in my original example. Now I have no idea why I did that on the first place. I have updated that comment to avoid misleading potential readers. Thank you! ...
written 13 months ago by Diego Diez700
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Comment: C: Comparison of Column of AnnotatedDataFrame
... Sorry if I look persistent on this but I didn't consider using $ or [[ as slot access. But maybe I am mistaken? I see (at least) three ways to access the data in the example above: tmp$Sepal.Length # use subsetting method. pData(tmp)$Sepal.Length # use accessor method then subsetting method. tmp@d ...
written 13 months ago by Diego Diez700
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Comment: C: Comparison of Column of AnnotatedDataFrame
... Thanks! Why is pData() preferred over slot access? ...
written 14 months ago by Diego Diez700
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Comment: C: Comparison of Column of AnnotatedDataFrame
... One more thought. I guess this behavior is also consistent with that of `data.frame(..., drop = FALSE)`. `[` will always return a data.frame, whereas `$` and `[[` return a vector. ...
written 14 months ago by Diego Diez700

Latest awards to Diego Diez

Popular Question 19 months ago, created a question with more than 1,000 views. For Get sequences for GRCh38 genome based on TxDb object locations
Popular Question 2.0 years ago, created a question with more than 1,000 views. For package built under R version 3.1.0 warning
Scholar 2.3 years ago, created an answer that has been accepted. For A: Can i set a path for readCodlinkSet()
Scholar 2.4 years ago, created an answer that has been accepted. For A: Can i set a path for readCodlinkSet()
Scholar 2.4 years ago, created an answer that has been accepted. For A: Can i set a path for readCodlinkSet()
Centurion 2.4 years ago, created 100 posts.
Voter 2.4 years ago, voted more than 100 times.
Supporter 3.1 years ago, voted at least 25 times.
Autobiographer 3.2 years ago, has more than 80 characters in the information field of the user's profile.

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