Hello there, I have 32 samples without any string 'treated' or something like this. File names are the sample names. In another csv file I have information about those count files (case/control). How can I load these files for differential expression analysis. In the vignettes, they used 'grep' and 'sub' for htseq output, I am not sure how can I adapt this to my dataset. 'https://www.bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#htseq'. I am new in rnaseq analysis. Any help? Best Regards Zillur
Thank you. I have managed to load the dataset. Now facing another problem.
I have tried
dds=dds[rowSums(counts(dds))>32,]
But the error persisits. the object is:Thanks again.
This is strange that every gene would contain a zero. What kind of data do you have? What are
colSums(counts(dds))
?Thank you. It turns out that one of my samples has zero for all genes. After removing that particular sample, its ok. Now I am having another problem in downstream analysis aka plotting.
I have updated geneplotter after facing the problem. But it didn't solve the error. I have updated it in the same session though. Thanks again and sorry to take your valuable time. Best Regards Zillur
If you encounter an error with a function, the best place to check is the help file:
?plotCounts
Take a look at the arguments, and make sure that you are providing the right ones.
Here R is giving you a clue, that you gave it a DESeqResults object and it that's not what it was expecting. What is the expected class of the first argument of
plotCounts
?Thank you. My bad! Its working. Many many thanks again. Best Regards, Zillur