Does anyone know how I can bypass the “subscript out of bounds” error on the plotting across all regions for the Flybase ID FBgn0283427 (FASN1). We have tried similar and different genes that have worked but this is the only one that we need that we can’t get the graph for.
I am taking the miniCURE at CCC
Jenna Nii and Alyssa Ware
Hi Jenna and Alyssa,
This error means that the gene is not found within the dataset. For example, trying to find it in the DESeq2 results table also brings up an empty table:
temp <- results(midgut, contrast = c("condition", "a1", "p1") )
R1_vs_R2 <- formatDESeq2Results(temp)
R1_vs_R2
my_gene <- filter(R1_vs_R2, GeneID=="FBgn0005590")
my_gene
0 rows
Is it a gene you found on FlyBase initially or did you encounter it somewhere else in the module?
Best,
Sayumi
Hello Sayumi, thank you for reaching out! it is a gene that we originally found on FlyBase and have also seen it throughout the tutorial in the module.
Apologies, I must have shared the wrong screenshot.
Here’s the search code for FBgn0283427.
There are genes that are in FlyBase that are not in the midgut dataset, and they could be there for either biological or technical reasons.
Biological: For example, we might imagine that there are genes specific to vision that will not show up in RNA-seq data in the gastrointestinal tract (in the same way that for humans rhodopsin would be expressed only in the eyes).
Technical: There could be issues with handling the tissue sample as it is being processed and prepared for sequencing, as well as biases in the machines used for PCR.
Because we can’t say whether or not the lack of data comes from biological or technical sources, we can’t conclude the expression of FBgn0283427 across the midgut is 0. We can only say that we don’t have it in our dataset.
I suggest finding another gene if possible that suits your story, as no data means no plot.
Thank you so much for the insight and providing some explanation behind that! We ended up choosing another gene so thank you 
