User: thokall

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thokall160
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Swedish Museum of Natural History
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Posts by thokall

<prev • 41 results • page 1 of 5 • next >
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Comment: C: EnsemblGene ID conversion
... It might be available otherwise one can generate one from the information at available at ensembl. See [here][1]. My experience is mostly from eukaryotes so I am not sure what the case is for bacteria [1]: https://www.bioconductor.org/packages/release/bioc/vignettes/ensembldb/inst/doc/ensembld ...
written 6 days ago by thokall160
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Answer: A: EnsemblGene ID conversion
... Hi, The information you need should be able to extract from the section "Using select with EnsDb packages" in the vignette to the package "AnnotationDbi". ...
written 7 days ago by thokall160
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Comment: C: how to remove degenerate sequence (N4) at the 5' and 3' of the reads?
... This forum is focused on answering question related to bioconductor packages. Cutadapt is not part of bioconductor and hence you are not likely to get much input here. ...
written 4 weeks ago by thokall160
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Comment: C: Creating an Expression Set from a csv file or EXCEL file
... You should be able to import the data with read.table and the settings more or less like the code you have. If it is truly an excel file you could go for the readxl package and read the excel file directly: library(readxl) # install with install.packages eset <- read_excel("file", skip ...
written 12 weeks ago by thokall160
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Comment: C: Creating an Expression Set from a csv file or EXCEL file
... You would get more input if you actually showed the code you have tried so far. Have you tried any of the steps described at https://bioconductor.org/packages/release/bioc/vignettes/Biobase/inst/doc/ExpressionSetIntroduction.pdf ? ...
written 12 weeks ago by thokall160
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Comment: C: Heatmap for ebseq2 output
... Your GenesOfInterest is not a vector, it is a data.frame that you created with the read.table function. You have to supply a vector to subset your matrix. In this case the data.frame is only one column wide, which means that it consists of a single vector. So your last command should be heatm ...
written 3 months ago by thokall160
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Answer: A: Heatmap for ebseq2 output
... Given how it is written I would think that it is subsetting the matrix to keep only genes that are of interested. Subsetting matrices in R is done with the syntax matrix[rows, columns], if 'rows' or 'columns' are left empty all rows/columns are returned. It could hence be a vector with True/False va ...
written 3 months ago by thokall160
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Answer: A: Why does limma voom E value give different result than the voom object
... The difference between your two examples are that you are using the complete Elist object from the voom function in the former and only the E slot of the same list in the later. By using only the normalized expression values you are not using all information from the voom function (see https://www.n ...
written 3 months ago by thokall160
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Answer: A: How to change font size in ClusterProfiler
... Hi, As far as I know clusterProfiler is using ggplot objects for plots. The par() function is used with the standard plotting functionality, but will not have any effect on ggplot plots. Try to read up on changing fonts when using ggplot2 and see if the functions for that can be used to modify the ...
written 3 months ago by thokall160
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Comment: C: Improving the performance of the align function from Rsubread for old Roche454 r
... Without a complete reference genome this figures are not in any way extreme in my eyes. Not very good that a large fraction of reads are not useful, but maybe the reads that do map are okay to use. In my experience both 454 and solid data are today seldom worth spending many hours on. ...
written 4 months ago by thokall160

Latest awards to thokall

Teacher 7 months ago, created an answer with at least 3 up-votes. For A: The query to the BioMart webservice returned an invalid result: the number of co
Scholar 11 months ago, created an answer that has been accepted. For A: Using R for EnrichR analysis
Scholar 21 months ago, created an answer that has been accepted. For A: Using R for EnrichR analysis
Scholar 21 months ago, created an answer that has been accepted. For A: Volcano Plot (highlighting top genes in a different color)

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