DE with edgeR package
0
0
Entering edit mode
4 months ago
Jimpix • 0

Hi, I have made the data with this command:

featureCounts -T 64 -p -t exon -g gene_name -a ~/data/human_genome_rf/Homo_sapiens.GRCh38.102.gtf -s 0 -o featureCounts_S_2.txt .bam .bam


I have .txt output, (not really readbly to paste in here) which I could read in R by DGEList() command. I would like to perform DE analysis and then make some plots and compairing. Coud anyone give me some advice how to parse that data? I d not know really what to do next to do it good.

expression edgeR level gene r • 651 views
1
Entering edit mode

https://www.bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf

It is outstandingly comprehensive. Please try that first and then ask a more specific question.

0
Entering edit mode

Thanks for reply, it means that for now my table of count is incorrect.

0
Entering edit mode

I do not know what that means.

0
Entering edit mode

If I want to perform DE analysis with edgeR, what kind of table (data) I have to had? I mean structure of data? Could you help? And if I have more than once sample (table with DE) how to compare it? Is that question is clear?

1
Entering edit mode
0
Entering edit mode

If I want to perform PCA from table of feature counts so from where can I take countdata and coldata?

0
Entering edit mode

I am not going to spoonfeed you. Read the linked thread and the edgeR manual. Really, it is all in there.

0
Entering edit mode

edgeR manual has no information about PCA. Coul you give me some tips from where can I get phenodata for hg38? with expression data will be enough? I think