xtail differential translation

[HazelStewart]

Hi,

I am running Xtail on some Ribosome Profiling data but I am struggling to understand the direction in which the genes are differentially translated.

I ran the package as follows:

mRNA_readcounts <- read.table("mRNA_readcounts_amalgamated.txt",
   header=T,row.names=1,stringsAsFactors = FALSE)

mrna <- mRNA_readcounts[,c(7,5,8,6)]
rpf <- mRNA_readcounts[,c(1,3,2,4)]

condition <- c("Infected","Mock","Infected","Mock")

results <- xtail(mrna,rpf,condition)
summary(results)

Are the genes with a positive log2fold change upregulated in the mock or infected samples?

Thanks very much

[YangLabProject]

Hi,
By default, Xtail use the first condition as the base level, so in your results, the positive log2fold value means the TE is upregulated in "mock" condition. You can set the "baseLevel" to change the default base level.

[trumanLuan]

Hi,
By default, Xtail use the first condition as the base level, so in your results, the positive log2fold value means the TE is upregulated in "mock" condition. You can set the "baseLevel" to change the default base level.

I've set baseLevel="NC" in my experiments. but in step 5, xtail returned error as following:
"Error in relevel.factor(colData(dataSet)$condition, baseLevel) :
'ref' must be an existing level"
Could you tell me what happened with the parameter?
I also tried to define "conditions" as a factor, but it still failed with the same error info.

Thanks in advance.

[GeegC]

Hi,
I have the same problem as @trumanLuan - please can you let me know if you found a solution?
Thanks