DEXSeq-Error in FUN(X[[i]], ...) : subscript out of bounds

[Giuseppe1995]

Hi
I'm having the same error of the author of this post, but my GTF file is not corrupted or whatever, and it has the same number of exonic regions as the number of lines of the count files (644354).
I am also following step by this tutorial.
Here, the code I used:

str(sampleTable)

'data.frame': 9 obs. of 2 variables: $ condition: chr "control"
"control" "control" "control" ... $ libType : chr "paired-end"
"paired-end" "paired-end" "paired-end" ...

flattenedFile

[1] "/Users/admin/GRCh37/genes.gff"

countFiles

[1] "16.EMATO-15.finalCount.txt" "16.EMATO-26.finalCount.txt" [3]
"16.EMATO-27.finalCount.txt" "16.EMATO-28.finalCount.txt" [5]
"16.EMATO-58.finalCount.txt" "16.EMATO-64.finalCount.txt" [7]
"16.GR2108-1.finalCount.txt" "16.GR2108-2.finalCount.txt" [9]
"16.GR2108-3.finalCount.txt"

To perform de analysis:

dxd <- DEXSeqDataSetFromHTSeq(
+    countFiles,
+    sampleData=sampleTable,
+    design= ~ sample + exon + condition:exon,
+    flattenedfile=flattenedFile )

I really can't figure out what's going on!
Thank you in advance,
Giuseppe

[kethselly]

Hello - I am having the same problem. Did you determine how to fix it?

[Giuseppe1995]

Tbh, I changed job 😂😂 Il giorno mer 31 gen 2024 alle 17:34 kethselly ***@***.***> ha scritto:

…

Hello - I am having the same problem. Did you determine how to fix it? — Reply to this email directly, view it on GitHub <#15 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ATRZNTKN3Y7CHCTMQSYZLPDYRJXDFAVCNFSM5XER27KKU5DIOJSWCZC7NNSXTN2JONZXKZKDN5WW2ZLOOQ5TCOJRHE2DONBUHEZA> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[kethselly]

Hope that job is going well! For anyone else - I was able to figure this out. See here. Apparently for some reason there were quotation marks around the gene:exon numbers in column one and when DEXSeq was importing the count data it actually put the data into three columns of a matrix instead of 2. So this wasn't actually loading the data correctly and was causing the error. The fix on the link above (at the bottom of the page) used sed to remove the quotes and output a new count file that could then be imported into DEXSEq.