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soheilazareie
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@soheilazareie-15508
Last seen 6.2 years ago
Canada, Vancouver, University of Britis…
Hello,
I would really appreciate if someone helps me understand my code better,
I need help with writing design formulas/matrix
is my coldata correct?...
I have 35 samples. Two different type of cell lines (which 2 or 3 of them have technical replicates as well) + control.
ac=15, dc=16, control=5
I would like to know what are the genes differentially expressed across two cell lines as well as comparing them with control.
my question is how should I make my formula for design to be able to comapre all samples against each other, like acianr versus control, ductal versuse acianr and ductal versus control,
here is my codes (DESeq.ds doesnt work),
read.counts<-read.csv("Data/ReadcountsC.csv", header = TRUE)
read_counts <- read.counts[,-1]
row.names(read_counts) <- read.counts[,1]
rownames(read_counts)
colnames(read_counts)
coldata<-read.csv("Data/phynotypeC.csv")
coldata=factor(coldata)
coldata = factor(coldata$treatment,levels = c("control", "Aci", "Duc"))
coldata
DESeq.ds <- DESeqDataSetFromMatrix ( countData = read_counts ,
colData = coldata_q,
design = ~ condition )
Note:
here is my excel file for coldata
| condition | treatment |
| Aci | AC1 |
| Aci | AC2 |
| Aci | AC3 |
| Aci | AC4 |
| Aci | AC5 |
| Aci | AC6 |
| Aci | AC7 |
| Aci | AC8 |
| Aci | AC9 |
| Aci | AC10 |
| Aci | AC11 |
| Aci | AC12 |
| Aci | AC13 |
| Aci | AC14 |
| Aci | AC15 |
| Duc | DC1 |
| uninjected | ctrl1 |
| Duc | DC3 |
| uninjected | ctrl2 |
| Duc | DC5 |
| Duc | DC6 |
| Duc | DC7 |
| uninjected | ctrl3 |
| Duc | DC9 |
| Duc | DC10 |
| Duc | DC11 |
| Duc | DC12 |
| Duc | DC13 |
| Duc | DC14 |
| Duc | DC15 |
| Duc | DC16 |
| uninjected | ctrl4 |
| Duc | DC18 |
| Duc | DC19 |
| Duc | DC20 |
| uninjected | ctrl5 |
Please post the error message if you had one.
Thanks for the reply.
here is one of the errors,
Error in `rownames<-`(`*tmp*`, value = colnames(countData)) :
attempt to set 'rownames' on an object with no dimensions
However, it looks like the above code now is working,
but the other problem that I have had is this code: plotMA (DGE.resultsa , alpha = 0.05 , main = "control vs. Ductal ",
ylim = c( -4 ,4))
Warning messages:
1: In plot.window(...) : "alpha" is not a graphical parameter
2: In plot.xy(xy, type, ...) : "alpha" is not a graphical parameter
3: In axis(side = side, at = at, labels = labels, ...) :
"alpha" is not a graphical parameter
4: In axis(side = side, at = at, labels = labels, ...) :
"alpha" is not a graphical parameter
5: In box(...) : "alpha" is not a graphical parameter
6: In title(...) : "alpha" is not a graphical parameter
NOTE: we are interested in seeing which genes are differentially expressed in our Ac versus DC samples compared to control(uninjected ones) and the same thing for control Vs Acinar and Ductal, so I am trying to use this code: res <- DGE.resultsa( coldata, contrast = c("condition", "Acinar", "Ductal") ), but again gives me this error: could not find function "DGE.resultsa", and not sure if the code is correct.
Thanks,
You can only use functions that are defined in the package. So results() is a function exported by DESeq2, and you can use that function, but there is no such function "
DGE.resultsa". That's why R is telling you it can't find this function.