Help with DESeq results to pathways with the fgsea package
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Gordon • 0
@4cb8e748
Last seen 2 days ago
United States

Hi, I am a totally new to R-studio and it's software. I have been trying to follow the tutorial posted on "https://stephenturner.github.io/deseq-to-fgsea/#load_some_results_from_deseq2"

I had used the using FGSEA package on, "https://bioconductor.org/packages/release/bioc/html/fgsea.html" and had followed the Installation for R.

1: Is there a more detail and step by step tutorial for this. I had found some but they required some knowledge of coding? 2: How do I import my own data into the software so the GSEA is shown as in website 1. 3: Here is an example of my data for GSEA:

#1.2                            
545 6                       
NAME    description WTcontrol1  WTcontrol2  WTcontrol3  WTDTnormalized1 WTDTnormalized2 WTDTnormalized3
ENSMUSG00000071103  1700029J07Rik   -0.2826271  0.03396225  -0.008006096    0.3456192   0.43789434  0.49301577
ENSMUSG00000100573  1700081H04Rik   -0.002503395    -0.01300478 0.002502918 -0.084319115    -0.0729208  -0.05217266
ENSMUSG00000097162  2310010J17Rik   -0.031499863    -0.18440628 -0.04216671 0.16484451  0.18860006  0.13092566
ENSMUSG00000032062  2310030G06Rik   -0.23690319 -0.21158266 -0.102458   0.16413021  0.24428272  0.31841516
ENSMUSG00000072852  2310040G07Rik   -0.03087902 -0.15501404 -0.079369545    0.268198    0.17418766  0.1296587
fgsea rna • 274 views
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@james-w-macdonald-5106
Last seen 2 days ago
United States

You don't want to use any 'normalized' data as input to DESeq2. Instead you want the raw counts/gene. There is a vignette for DESeq2 that you can read, as well as a vignette for fgsea, both of which are tutorials that are meant to help people get started.

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I am currently stuck on

library(DESeq2)

library(airway) ddsSE <- DESeqDataSet(airway, design = ~ cell + dex) ddsSE <- DESeq(ddsSE) res <- results(ddsSE, tidy = TRUE) readr::write_csv(res, path="data/deseq-results-tidy-human-airway.csv")

What are the options to replace "airway" with so I can run my own sample opposed to library(tidyverse) res <- read_csv("data/deseq-results-tidy-human-airway.csv") res

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The option is to point to your own data rather than using demo data. Have you read the DESeq2 vignette I pointed to?

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Thanks for the assist. Do you know how to decrease the font of the pathway so it is more legible?

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If you are talking about the ggplot part, then yes. See ?theme, in particular the axis.text.y argument, as well as ?element_text.

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