Hi all,
I was wondering if anybody could help. I have relatively simple problem, but can't seem to figure out the solution. I am trying to subset some data from a GSE sequencing data that contains 100+ sequencing samples. I am subsetting based on tissue type (and normal vs tumor).
The problem I am having is as follows: I am trying to subset two conditions from one tissue (age). Neonatal liver and adult liver. Which are named as "neonatal liver" or just "liver" for the adult liver. I am subsetting through a slot (source_name) that contains this information as follows:
gse<-getGEO("GSE78076", GSEMatrix = TRUE, getGPL = FALSE)
gse<-gse[[1]]
head(gse)
subset<- gse[,65:103]
subset
levels(subset$source_name_ch1)
lvls<-c("liver", "neonatal liver")
lvls
es<-subset[,subset$source_name_ch1 %in% lvls]
table(lvls)
boxplot(es)
es$source_name_ch1<-factor(es$source_name_ch1, levels = lvls)
es$source_name_ch1
es$source_name_ch1
[1] liver liver liver liver liver liver liver liver liver liver
[11] liver liver liver liver neonatal liver neonatal liver neonatal liver
Levels: liver neonatal liver
This works fine and subsets the data into neonatal liver and adult liver. Within "liver" however, there are different treatments. normal adult liver, or liver that has been treated with a damaging agent. This is all named as "liver"
Information about the the damaging agent vs non damaging agent is in a different slot, es$description, and I am having trouble subsetting my data based on these two slots so that I can actually tease apart neonatal liver, adult liver, and then liver treated with the damaging agent.
es$description
V69 V70 V71 V72 V73
primary cells, normal primary cells, normal primary cells, normal primary cells, normal primary cells, normal
V74 V75 V76 V77 V78
primary cells, DDC-treated primary cells, DDC-treated primary cells, DDC-treated primary cells, DDC-treated primary cells, DDC-treated
V79 V80 V81 V82 V87
primary cells, DDC-treated primary cells, DDC-treated primary cells, DDC-treated primary cells, DDC-treated primary cells, normal
V88 V89
primary cells, normal primary cells, normal
Levels: metastatic tumor primary cells, DDC-treated primary cells, normal primary tumor
>
Can somebody please help subset my subset even further to now separate the adult liver from damaged liver which are all currently labelled as just liver as now I am struggling to make the correct comparisons!
Thank you in advance and apologies if any of the code is out of place/you need further information as I am new to this. I'd be happy to provide any further information! I have looked for a solution to this but as far as I can search I cannot find what I am looking for, so apologies if this has been answered before!
Many thanks!
Awesome! Thank you so much for clearing that up, and yes will save these R related questions for those forums. Many thanks again!
A