Error when running "SalmonTE.py test"

[Wen-Wei Liao]

Hi there,

Thanks for developing SalmonTE! It's really fast and suitable for large-scale project.
But I got an error when running SalmonTE.py test:

Error in FUN(X[[i]], ...) :
  assay colnames() must be NULL or equal colData rownames()
Calls: SalmonTE ... SummarizedExperiment -> SummarizedExperiment -> .local -> vapply -> FUN

Here is a possible solution I found. I hope it's helpful.
By the way, I use R version 3.4.1.

Best,
Wen-Wei

[Hyun-Hwan Jeong]

Dear @wwliao,

I am happy to hear you like the SalmonTE! To solve the issue properly, I may need your input, so could you answer my questions if you are fine?

• How many replicates were used in your experiments?
• Which type of analysis did you try to run? Was it regression or differential expression analysis?
• Did you generate a custom reference library?
• If you don't mind, can you send your expr.csv and phenotype.csv to my email ([e-mail])? Those files will be used for a debugging, and I will promise I will completely remove the file. If you don't want then you can tell me a brief description of the files, like how many records and columns are in the files. This will help me.

Best,

Hyun-Hwan Jeong

[Wen-Wei Liao]

Thanks for your prompt reply!
I used the following commands to run SalmonTE:

$ SalmonTE.py quant --reference=hs --exprtype=count data
$ SalmonTE.py test --inpath=SalmonTE_output --outpath=tmp --tabletype=csv --figtype=png

• 8 replicates for each condition
• I'd like to do the differential expression analysis
• No, I used the reference provided by SalmonTE
• I just sent you the files

Best,
Wen-Wei

[Hyun-Hwan Jeong]

@wwliao, This problem happened because my code did not handle the sample names with a hyphen, but not I have fixed the code, so I believe you are fine now.

Please pull the changes and run the test mode again.

Best,

Hyun-Hwan

[Wen-Wei Liao]

It works!
Thanks for your kind help.

Wen-Wei

[Hyun-Hwan Jeong]

You’re welcome! Thanks for the reporting!