I am trying to make plots by CummeRbund using Cuffdiff outputs I got from Galaxy. However when I loaded data into RStudio using "readCufflinks" function, it requires "run.info file" and "read_groups info file". Actually I could get a volcano plot without these files. But I failed to make MDS plot or PCA plot once requires replicates information (see code below). I was thinking should these two files include my experiment replicates information, which leads to the fail. Therefore, where can I find these files from galaxy, they are not in the Cuffdiff output file list (https://ibb.co/frGGey).
setwd("/Users/Cmengni/Desktop/LSTM/Project/Galaxy resutlts/IT4 Var14 HBMEC TNF 0h_2h/Cuffdiff copy/cuff output/") library(cummeRbund) cuff <- readCufflinks() cuff CuffSet instance with: 2 samples 66009 genes 215942 isoforms 197589 TSS 89716 CDS 65906 promoters 197589 splicing 22640 relCDS gene.PCA <- PCAplot(genes(cuff), "PC1", "PC2") Warning: Ignoring unknown aesthetics: label gene.PCA genes.PCA.rep <- PCAplot(genes(cuff), "PC1", "PC2",replicates = T) Error in result_create(conn@ptr, statement) : near "from": syntax error
And I find a web page mentioned that there is a Galaxy tool package generate output can be used directly in CummeRbund (https://toolshed.g2.bx.psu.edu/repos/jjohnson/cummerbund). But I am very new in bioinformatics and could not understand how can can fix this.
I would really appreciate any help.