User: thokall

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thokall160
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160
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Location:
Swedish Museum of Natural History
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nucdiv
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4 days ago
Joined:
1 year, 10 months ago
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Posts by thokall

<prev • 41 results • page 2 of 5 • next >
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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 5 months 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 12 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 12 months ago by thokall160
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Comment: C: Using Limma to normalize data sets
... I have tried your code and I do not have this issue. Below is the output from your code block on my machine. Since I can not reproduce your problem it is hard to know what is going on, but I suggest you double-check that you have the latest version of bioconductor and updated versions of all the pac ...
written 12 months ago by thokall160
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Comment: C: Using Limma to normalize data sets
... Check that your working directory contain the files of interest or modify your code to contain the complete path downloadedAffyFiles <- list.files("~/Downloads/GSE53454_RAW/", pattern = "CEL.gz", full.names=TRUE)   ...
written 12 months ago by thokall160
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Comment: C: Using Limma to normalize data sets
... you need to untar the downloaded object so that you can see the files that this archive contains. If you look at the command given in the limma manual it supplies the character vector to the argument filenames (sorry if I confused you earlier). If your files are in "Data/GSE53454_RAW" you can list ...
written 12 months ago by thokall160
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Comment: C: Using Limma to normalize data sets
... The second examples uses the ReadAffy function that Will import Affymetrix data. The function need a Vector of filenames to read (in the exemple this information stored in target$FileName. You can hence download the files you are interested (the .cel files) and create a vector with these file names ...
written 12 months ago by thokall160
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Answer: A: Using Limma to normalize data sets
...   The limma manual has information on importing and analysing Affymetrix data. The second example in section 3.2 contains some basic info. If you are struggling with something more specific please include the code that you have tried so far, as that makes it easier to help out.   ...
written 12 months ago by thokall160
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Comment: C: How can I do a correlation heatmap between two groups of matrices (metabolomic a
... Hi, As you are not providing any code that you have tested nor name any packages that you have looked at it is hard to see that this is directly related to bioconductor. For a general description on how to generate a heatmap have a look at https://www.r-bloggers.com/how-to-make-a-simple-heatmap-in- ...
written 15 months ago by thokall160
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Comment: C: how to create csv file with name of gene from unique ID of lcpm ?
... If you in an interactive r session do your analysis and type y2$genes you will see that this is not a vector. You hence have to select one of the columns (= a vector) of this dataframe to use as row names. ...
written 17 months ago by thokall160

Latest awards to thokall

Teacher 8 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 12 months ago, created an answer that has been accepted. For A: Using R for EnrichR analysis
Scholar 22 months ago, created an answer that has been accepted. For A: Using R for EnrichR analysis
Scholar 22 months ago, created an answer that has been accepted. For A: Volcano Plot (highlighting top genes in a different color)

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