User: Diego Diez

gravatar for Diego Diez
Diego Diez730
Reputation:
730
Status:
Trusted
Location:
Japan
Website:
http://qimm.ifrec.osak...
Scholar ID:
Google Scholar Page
Last seen:
2 months, 1 week ago
Joined:
14 years, 4 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 • 161 results • page 1 of 17 • next >
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Answer: A: How to process Codelink UniSet Rat I Bioarray data
... The file format of the expression data is not in Codelink format. In particular, none of the columns expected to contain signal information are there. This may seem confusing but there is a distinction between the microarray platform (Codelink) and the software used to process the microarrays (?). T ...
written 7 months ago by Diego Diez730
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Comment: C: How to process Codelink UniSet Rat I Bioarray data
... In addition to considering what James points out in his response, it is not clear why do you need to call readCodelinkSet() and readCodelink() in your code. Is this a publicly accessible dataset (e.g. GEO) for which you could share with us the URL to check it? ...
written 7 months ago by Diego Diez730
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Answer: A: How to check if the microarray data is from codelink
... Unfortunately it is not possible to identify Codelink files using the extension. Usually they are named either TXT or txt but that is not very informative because that extension is commonly used for regular text files. A Codelink file has to contain a header formatted in a particular way. Also, it b ...
written 9 months ago by Diego Diez730
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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 19 months ago by Diego Diez730
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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 19 months ago by Diego Diez730
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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 19 months ago by Diego Diez730
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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 23 months ago by Diego Diez730
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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 2.0 years ago by Diego Diez730
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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 2.0 years ago by Diego Diez730
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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 2.0 years ago by Diego Diez730

Latest awards to Diego Diez

Popular Question 2.5 years ago, created a question with more than 1,000 views. For Get sequences for GRCh38 genome based on TxDb object locations
Popular Question 2.9 years ago, created a question with more than 1,000 views. For package built under R version 3.1.0 warning
Scholar 3.2 years ago, created an answer that has been accepted. For A: Can i set a path for readCodlinkSet()
Scholar 3.3 years ago, created an answer that has been accepted. For A: Can i set a path for readCodlinkSet()
Scholar 3.3 years ago, created an answer that has been accepted. For A: Can i set a path for readCodlinkSet()
Centurion 3.3 years ago, created 100 posts.
Voter 3.3 years ago, voted more than 100 times.
Supporter 4.0 years ago, voted at least 25 times.
Autobiographer 4.1 years ago, has more than 80 characters in the information field of the user's profile.

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