Help with DESeq results to pathways with the fgsea package
1
0
Entering edit mode
Gordon • 0
@4cb8e748
Last seen 7 months 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 • 1.0k views
ADD COMMENT
0
Entering edit mode
@james-w-macdonald-5106
Last seen 13 hours 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.

0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 811 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6