User: thokall

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thokall160
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Swedish Museum of Natural History
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Posts by thokall

<prev • 38 results • page 1 of 4 • next >
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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 4 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 4 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 5 weeks 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 5 weeks 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 5 weeks 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 7 weeks 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 9 weeks ago by thokall160
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Comment: C: Improving the performance of the align function from Rsubread for old Roche454 r
... I do not have any idea on to weather the alignment step could be improved on 454 data, but I have seen o few data set with low proportion of mapped reads and just want to highlight that there are many plausible explanation that perhaps should be explored before looking at the alignment/counting appr ...
written 10 weeks ago by thokall160
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Comment: C: Multiple alignment of big DNA sequences files
... Hi, Are you sure that there is a meaningful alignment that can be created for these sequences? I do not think this is an easy task in R or in any other language. There are large number of softwares and approaches to multiple alignments that might be of help. Most of these are not part of bioconduct ...
written 9 months ago by thokall160
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Comment: C: Using Limma to normalize data sets
... Since I can not reproduce your problems I can not really be of much help here, besides trying to install packages that fails on your own and then use the vignette of gcrma to see how to use this package efficiently. Good luck! ...
written 9 months ago by thokall160

Latest awards to thokall

Scholar 9 months ago, created an answer that has been accepted. For A: Using R for EnrichR analysis
Scholar 20 months ago, created an answer that has been accepted. For A: Using R for EnrichR analysis
Scholar 20 months ago, created an answer that has been accepted. For A: Volcano Plot (highlighting top genes in a different color)

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