Hello everybody! I have a question about an analysis of my polysome profiling experiment. In my case I have to conditions (with and without treatment) and two sample types for each condition, the mRNAs bound to the monosomal fractions (only to a single ribosome, or its preinitiation forms) and mRNAs bound to polysomal fractions (more than one ribosome). I want to compare the translation efficiency, that is defined as the ratio between the polysomal/monosomal lectures os each gene, in my treatmets, so I think I have to do a ratio of ratios. I also want to add the bath effect due to each sample type is from the same sample, and I have replicates. I'm using DESeq2, and my script is:
data <- DESeqDataSetFromMatrix(countData = countData,colData = colData,design = ~ batch + sampleType + condition + sampleType:condition) dds <- DESeq(data, reduced = ~ batch + condition + sampleType, test="LRT")
I'm not sure if I'm doing properly. Also, I don't undestand at all what's the meaning of the log2foldchange and the pvales that the DESeq2 returns for this analysis, because I read that for the LTR test there are no direct correlation between them, so I'm not sure how to interpret them.
Thank you very much in advance!!