So I am using Proteoviz for my phosphoproetmics project. In our run, there was no pool sample because there was a single kit used for all samples (they were below 20)
So I need to skip the normalization by Pool and only normalize the batch effects between the two technical replicates/two runs.
I therefore need to change the part of the second code here!
I would imagine this should do the job it.
df2n <- df2 %>%
right_join(sample_df) %>%
group_by(id, Batch) %>%
mutate(Intensity = Intensity - median(Intensity, na.rm = TRUE)) %>%
ungroup()
Hello,
So I am using Proteoviz for my phosphoproetmics project. In our run, there was no pool sample because there was a single kit used for all samples (they were below 20)
So I need to skip the normalization by Pool and only normalize the batch effects between the two technical replicates/two runs.
I therefore need to change the part of the second code here!
df2n <- df2 %>% right_join(sample_df) %>% group_by(id, Batch) %>% mutate(Intensity = Intensity - mean(Intensity[which(Pool == "POOL")])) %>% group_by(Sample) %>% mutate(Intensity = Intensity - median(Intensity, na.rm = TRUE)) %>% ungroup()
I would imagine this should do the job it. df2n <- df2 %>% right_join(sample_df) %>% group_by(id, Batch) %>% mutate(Intensity = Intensity - median(Intensity, na.rm = TRUE)) %>% ungroup()
Or am I mistaken?
Thanks a lot in advance, Best, Moustafa