Entering edit mode
2.3 years ago
Jimpix
▴
10
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.
Please help.
Did you read the manual?
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.
Thanks for reply, it means that for now my table of count is incorrect.
I do not know what that means.
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?
Using featureCounts Output for DE analysis in edgeR
If I want to perform PCA from table of feature counts so from where can I take countdata and coldata?
I am not going to spoonfeed you. Read the linked thread and the edgeR manual. Really, it is all in there.
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