Error IsoformSwitchAnalyzeR with kallisto data and ensembl annotation gtf

Question

[dina.hesham139]

Hi, I 'm trying to analyze my kallisto data with IsoformSwitchAnalyzeR but I get this error when I use the importRdata function, I get this error:

> aSwitchList <- importRdata(
+   isoformCountMatrix   = mySwitchList$counts,
+   isoformRepExpression = mySwitchList$abundance,
+   designMatrix         = designMatrix,
+   isoformExonAnnoation = "/rice/Oryza_sativa.IRGSP-1.0.37.gtf",
+   showProgress = T)
Step 1 of 6: Checking data...
Step 2 of 6: Obtaining annotation...
    importing GTF (this may take a while)
converting annotated CDSs
Error in importRdata(isoformCountMatrix = mySwitchList$counts, isoformRepExpression = mySwitchList$abundance,  : 

The annotation and quantification (count/abundance matrix and isoform annotation) seems to be different (jacard similarity < 0.95). 
Either isforoms found in the annotation are not quantifed or vise versa. 
Specifically:
 42346 isoforms were quantified.
 98663 isoforms are annotated.
 Only 42346 overlap.

This combination cannot be analyzed since it will cause discrepencies between quantification and annotation thereby skewing all analysis.

Please make sure they belong together and try again. For more info see the FAQ in the vignette.

[Kristoffer Vitting-Seerup]

Could you update to IsoformSwitchAnalyzeR 1.5.11 (remember to restart R after installation) and try again?

[dina.hesham139]

I will try Thank you!

[Kristoffer Vitting-Seerup]

Let me know if you run into more troubles :-)

[harry]

I also have same problem and i have latest version then why is it show this error

[Kristoffer Vitting-Seerup]

If you use the latest version of IsoformSwitchAnalyzeR it gives this error because the files provided does not match. If you want help looking more into it please don't hesitate to ask in the google group or github - and remember to provide more information about which files you are using - the code you run and the actual error message you get.

Answer 1

[liuwei]

My R version was 3.5.1, however, I cann't install IsoformSwitchAnalyzeR 1.5.11 or IsoformSwitchAnalyzeR 1.6.0 with conda

[Kristoffer Vitting-Seerup]

For R-3.5.1 you can get IsoformSwitchAnalyzeR 1.5.11 from github via the following command:

if (!requireNamespace("devtools", quietly = TRUE)){
    install.packages("devtools")
}
devtools::install_github("kvittingseerup/IsoformSwitchAnalyzeR", build_vignettes = TRUE)