User: arfranco

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arfranco130
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Posts by arfranco

<prev • 37 results • page 2 of 4 • next >
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Comment: C: Very small bug in DESeq2
... Well, look at this code > source("https://bioconductor.org/biocLite.R") Bioconductor version 3.3 (BiocInstaller 1.22.3), ?biocLite for help > biocLite("pasilla") BioC_mirror: https://bioconductor.org Using Bioconductor 3.3 (BiocInstaller 1.22.3), R 3.3.1 (2016-06-21). Installing package(s) ‘ ...
written 3.0 years ago by arfranco130
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Answer: A: Very small bug in DESeq2
... I installed the pasilla package with a direct install.package('pasilla') command after defining the bioclite repository with the R command setRepositories() I don't have DESeq package installed, and I know this is actually the problem This is a minor problem, though. It simply represented a seri ...
written 3.0 years ago by arfranco130
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Very small bug in DESeq2
... I am trying to teach my students the using of DESeq2, and they are repeating the instructions contained into the vignette  And they have found a very small bug. This bug does not appear when the "old" DESeq is installed into your system. But since DESeq2 is recommended, I insisted my students to no ...
software error written 3.0 years ago by arfranco130
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Answer: A: Limma Elist subsetting
... I forgot to mention I tried that solution as well, but it is not working (is not subsetting) subset <- data[data$E >= 2.3,] Error in object[[a]][i, j, drop = FALSE] : (subscript) logical subscript too long ...
written 3.4 years ago by arfranco130
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Limma Elist subsetting
... I am running a microarray analysis using limma containing some spike-in controls that allowed me to know that I got a linear signal response with a data$E >= 2.3, where data is a EList class object (data is microarray data already substracted and normalized), and data$E contains the intensity sig ...
microarray limma subsetting written 3.4 years ago by arfranco130
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Answer: A: Methylation and gene expression data
... I assume you want R packages https://www.bioconductor.org/packages/release/BiocViews.html#___DifferentialMethylation Anf these as well https://www.bioconductor.org/packages/release/BiocViews.html#___DNAMethylation ...
written 3.4 years ago by arfranco130
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Comment: C: Error: could not find function "HTSeqCounts"
... And this is written in that vignette about HTSeq The initial steps of a DEXSeq analysis, described in the following two sections, is typically done outside R, by using two provided Python scripts ...
written 3.5 years ago by arfranco130
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Answer: A: Error: could not find function "HTSeqCounts"
... read.HTSeqCounts() is indeed the function implemented into R that reads the counts that you have previously obtained using HTSeqCount. If you have not run HTSeqCount, you have not counts to read I know for sure that HTSeqCount is a standalone application. After reading the vignette and looking into ...
written 3.5 years ago by arfranco130
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Answer: A: Error: could not find function "HTSeqCounts"
... HTSeqCount is not part of the DEXSeq package. I have just installed this package and check it. I have also run a search in the pdf vignette and HTSeqCount is not defined within the document You probably need to install and use HTSeqCount outside R. This happens with limma, DESeq, DESeq2, etc ...
written 3.5 years ago by arfranco130
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Answer: A: How to import data to R
... If you want to import data from excel files, you can do it  library(gdata) data <- read.xls(xls="Your_file.xls", sheet = 1, header = TRUE) # You can choose different sheet and have other choices This library is very straightforward and stable, working very well ...
written 3.6 years ago by arfranco130

Latest awards to arfranco

Great Question 2.5 years ago, created a question with more than 5,000 views. For limma p-value and adjusted p-value meaning
Popular Question 2.5 years ago, created a question with more than 1,000 views. For limma p-value and adjusted p-value meaning
Popular Question 3.5 years ago, created a question with more than 1,000 views. For limma p-value and adjusted p-value meaning
Scholar 3.8 years ago, created an answer that has been accepted. For A: matrix transposing in R
Supporter 3.9 years ago, voted at least 25 times.
Scholar 4.3 years ago, created an answer that has been accepted. For A: matrix transposing in R
Scholar 4.3 years ago, created an answer that has been accepted. For A: matrix transposing in R

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