Question: Error IsoformSwitchAnalyzeR with kallisto data and ensembl annotation gtf
gravatar for dina.hesham139
12 months ago by
dina.hesham139120 wrote:

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. 
 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.
ADD COMMENTlink modified 10 months ago by harry10 • written 12 months ago by dina.hesham139120

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

ADD REPLYlink written 12 months ago by kristoffer.vittingseerup3.2k

I will try Thank you!

ADD REPLYlink modified 12 months ago • written 12 months ago by dina.hesham139120

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

ADD REPLYlink written 12 months ago by kristoffer.vittingseerup3.2k

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

ADD REPLYlink written 10 months ago by harry10

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.

ADD REPLYlink written 10 months ago by kristoffer.vittingseerup3.2k
gravatar for liuwei
11 months ago by
liuwei0 wrote:

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

ADD COMMENTlink written 11 months ago by liuwei0

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

if (!requireNamespace("devtools", quietly = TRUE)){
devtools::install_github("kvittingseerup/IsoformSwitchAnalyzeR", build_vignettes = TRUE)
ADD REPLYlink written 11 months ago by kristoffer.vittingseerup3.2k
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