User: thokall

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thokall120
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Location:
Swedish Museum of Natural History
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nucdiv
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4 days, 10 hours ago
Joined:
10 months, 3 weeks ago
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Posts by thokall

<prev • 29 results • page 1 of 3 • next >
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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 20 days ago by thokall120
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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 20 days ago by thokall120
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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 20 days ago by thokall120
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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 20 days ago by thokall120
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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$FileName. You can hence download the files you are interested (the .cel files) and create a vector with these file names ...
written 20 days ago by thokall120
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Answer: A: Using Limma to normalize data sets
...   The limma manual has information on importing and analysing Affymetrix data. The second example in section 3.2 contains some basic info. If you are struggling with something more specific please include the code that you have tried so far, as that makes it easier to help out.   ...
written 20 days ago by thokall120
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Comment: C: How can I do a correlation heatmap between two groups of matrices (metabolomic a
... Hi, As you are not providing any code that you have tested nor name any packages that you have looked at it is hard to see that this is directly related to bioconductor. For a general description on how to generate a heatmap have a look at https://www.r-bloggers.com/how-to-make-a-simple-heatmap-in- ...
written 12 weeks ago by thokall120
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Comment: C: how to create csv file with name of gene from unique ID of lcpm ?
... If you in an interactive r session do your analysis and type y2$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 5 months ago by thokall120
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Comment: C: use deseq2 in asthma
... You will likely get better answers if you show the code you have tried so far and the errors that it generates. If you mean the package Genomicfeatures you should be able to follow the instructions at https://bioconductor.org/packages/release/bioc/html/GenomicFeatures.html ...
written 5 months ago by thokall120
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Answer: A: package DESeq2 installation with R.
... DESeq2 is part of bioconductor and can be Installed according to the instructions that you find here https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html ...
written 6 months ago by thokall120

Latest awards to thokall

Scholar 10 months ago, created an answer that has been accepted. For A: Using R for EnrichR analysis
Scholar 10 months ago, created an answer that has been accepted. For A: Volcano Plot (highlighting top genes in a different color)

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