# IsoformSwitchAnalyzR - "longer object length is not a multiple of shorter object length"

**URL:** <https://help.galaxyproject.org/t/isoformswitchanalyzr-longer-object-length-is-not-a-multiple-of-shorter-object-length/10276>\
**Category:** usegalaxy.eu support\
**Tags:** gtn-tutorial, transcriptomics, stringtie\
**Created:** [June 18, 2023, 4:42am UTC](https://help.galaxyproject.org/t/isoformswitchanalyzr-longer-object-length-is-not-a-multiple-of-shorter-object-length/10276 "2023-06-18T04:42:31Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![Margaret\_M](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/margaret_m/32/4432_2.png) [@Margaret\_M](https://help.galaxyproject.org/u/Margaret_M)\
**Post date:** [June 18, 2023, 4:42am UTC](https://help.galaxyproject.org/t/isoformswitchanalyzr-longer-object-length-is-not-a-multiple-of-shorter-object-length/10276/1 "2023-06-18T04:42:31Z")

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Hello! I am trying to use this tool to compare differences in two conditions across three samples. I get the following error message when trying to import my data:

“reading in files with read\_tsv  
1 2 Error in tximport::tximport(files = localFiles, type = tolower(dataAnalyed$orign), :  
all(txId == raw[[txIdCol]]) is not TRUE  
Calls: importIsoformExpression → → stopifnot  
Warning message:  
In txId == raw[[txIdCol]] :  
longer object length is not a multiple of shorter object length”

The error message suggests that I have duplicate input datasets, but I do not - they’re three different inputs per condition.

I performed transcriptome assembly using the following tutorial and I don’t know if this is part of the issue?

> **[Galaxy Training: Genome-wide alternative splicing analysis](https://training.galaxyproject.org/topics/transcriptomics/tutorials/differential-isoform-expression/tutorial.html#isoform-switching-analysis-with-isoformswitchanalyzer)**
>
> Training material for all kinds of transcriptomics analysis.

My history:

> **[Galaxy
            | Europe](https://usegalaxy.eu/published/history?id=b7b3102ddb80500c)**
>
> Galaxy is a community-driven web-based analysis platform for life science research.

Any help is greatly appreciated!

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<div class="post-metadata">

**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [June 20, 2023, 10:43pm UTC](https://help.galaxyproject.org/t/isoformswitchanalyzr-longer-object-length-is-not-a-multiple-of-shorter-object-length/10276/2 "2023-06-20T22:43:08Z")

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Hi @Margaret_M

Notice how the transcripts are named in the Stringtie files – they are using the default transcript names generated for novel transcripts by that tool. These instead need to match up with the reference annotation’s transcript\_id attributes and the \>lines in the transcript fasta.

It looks like you missed a step that consolidates that data: **Stringtie merge**. Scroll up in the tutorial to find it.

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<div class="post-metadata">

**Author:** ![Margaret\_M](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/margaret_m/32/4432_2.png) [@Margaret\_M](https://help.galaxyproject.org/u/Margaret_M)\
**Post date:** [July 4, 2023, 11:12am UTC](https://help.galaxyproject.org/t/isoformswitchanalyzr-longer-object-length-is-not-a-multiple-of-shorter-object-length/10276/3 "2023-07-04T11:12:09Z")

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Thank you very much. I have a new error, but this at least solves that one