Re: [R] RNA Seq Analysis in R

2020-08-01 Thread Rasmus Liland
On 2020-08-01 15:52 -0400, Matthew McCormack wrote: | On 8/1/20 1:13 PM, Jeff Newmiller wrote: | | On August 1, 2020 4:01:08 AM PDT, Anas Jamshed wrote: | | | I performed this in GEO2R and find | | | R script there and Runs R script Anas, how did you come up with this script at all by reading t

Re: [R] RNA Seq Analysis in R

2020-08-01 Thread Matthew McCormack
As with the previous post, I agree that Bioconductor will be a better place to ask this question. As a quick thought you also might try to adjust the p-value in the last line: DEGs = subset(tT, P.Value < 0.01 & abs(logFC) > 2). You could play around with the P.Value, 0.01 is pretty low, you co

Re: [R] RNA Seq Analysis in R

2020-08-01 Thread Jeff Newmiller
https://www.bioconductor.org/help/ On August 1, 2020 4:01:08 AM PDT, Anas Jamshed wrote: >I choose microarray data GSE75693 of 30 patients with stable kidney >transplantation and 15 with BKVN to identify differentially expressed >genes >(DEGs). I performed this in GEO2R and find R script there a

[R] RNA Seq Analysis in R

2020-08-01 Thread Anas Jamshed
I choose microarray data GSE75693 of 30 patients with stable kidney transplantation and 15 with BKVN to identify differentially expressed genes (DEGs). I performed this in GEO2R and find R script there and Runs R script Successfully on R studio as well. The R script is : # Differential expression