Entering edit mode
4.0 years ago
n.tear
▴
80
Hi,
I am trying to export my RNAseq results with glimma and I am following this workshop (https://bioconductor.github.io/BiocWorkshops/rna-seq-data-analysis-with-deseq2.html#building-reports) unfortuneatly I am geting an error as per the title.
Please would someone be able to educate me as to why this is occuring? My code below:
#Glimma
library(org.Hs.eg.db)
res.s$symbol <- mapIds(org.Hs.eg.db,keys = rownames(res.s),column = "SYMBOL",keytype="ENSEMBL")
table(rownames(res.s) %in% keys(org.Hs.eg.db, "ENSEMBL"))
library("Glimma")
tmp <- "Z:/R.DESeq2"
status <- as.numeric(res.s$padj < .1)
anno <- data.frame(GeneID=rownames(res.s), symbol=res.s$symbol)
glMDPlot(res.sLFC, status=status, counts=counts(dds.s,normalized=TRUE),
groups=dds.s$comparison, transform=FALSE,
samples=colnames(dds.s), anno=anno,
path=tmp, folder="glimma", launch=FALSE)
Error in [.data.frame
(res.df, , cols) : undefined columns selected
Many thanks in advance Nathan
Hello Nathan. What is the output of:
?
Hi Kevin thank you for your reply
Should
res.sLFC
not just be a data-frame? - and you will have to specify the x and y values viaxval
andyval
, respectively.I generated the res.sLFC using:
As a data frame:
Now I have changed toa data frame the error is:
I see. You will have to also set the following:
In fact, you may even have to create a new column for the logged base mean, and then use that:
Hi Kevin, many thanks for your continued support.
Unfortunately I am still having no luck
Seems that there are missing or infinite values in your logmean variable. Can check the output of this:
output suggests not
Can you literally check your input data, in both formatting (string, numeric, factor, etc) and also for other missing values? Like, literally, look through it or output it to disk and open it in Excel.
Yes looked in exel and no missing values and checked the class of each column in res.sLFCdf and they are correct
could it be an issue that not all the rownames of res.s are in org.Hs.eg.db when I make the anno?
I also have some NAs in my status object. could this be a problem?
Did you manage to get any further with this? I am limited in what I can do from a distance. Best idea would be to find the last known working example, and then work from there
Hi Kevin,
Thanks for your help. Ive done exacly as you have said above and managed to work it out in the end.
Cheers
Nathan