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Help with Cuffdiff output and CummeRbund
Dear community,
I have RNA-seq data of 3 different samples, mock, condition 1 and condition 2. I have used the tuxedo suite for my analysis. I bypassed cuffmerge and used only cuffcompare. I finished with cuffdiff. The cuffdiff output looks perfect, all the files are there. The problem lies with cummeRbund. After making my cuffData.db file I immediately receive 22 warnings. I went back to my cuffdiff results (gene_exp.diff and cds_exp.diff file) and saw that they had "-inf" and "=-nan" values in log2(fold change) and test_stat column.
How can I have so many errors when I ran everything in the correct way? I ran cufflinks and tophat with an annotation file and I have proper files (seemingly proper files) for everything up until cuffdiff. I don't know how to circumvent these Nan or inf values for visualization in cummeRbund. I can get an adobe pdf of various plots, but they are damaged files and can't be repaired and therefore not viewed. My organism is Arabidopsis thaliana.
Any help would be appreciated.
I have RNA-seq data of 3 different samples, mock, condition 1 and condition 2. I have used the tuxedo suite for my analysis. I bypassed cuffmerge and used only cuffcompare. I finished with cuffdiff. The cuffdiff output looks perfect, all the files are there. The problem lies with cummeRbund. After making my cuffData.db file I immediately receive 22 warnings. I went back to my cuffdiff results (gene_exp.diff and cds_exp.diff file) and saw that they had "-inf" and "=-nan" values in log2(fold change) and test_stat column.
How can I have so many errors when I ran everything in the correct way? I ran cufflinks and tophat with an annotation file and I have proper files (seemingly proper files) for everything up until cuffdiff. I don't know how to circumvent these Nan or inf values for visualization in cummeRbund. I can get an adobe pdf of various plots, but they are damaged files and can't be repaired and therefore not viewed. My organism is Arabidopsis thaliana.
Any help would be appreciated.