condition problems

[nrius]

Hi! quant created a condition.csv file, but since in the README says that it should be called control.csv I made the modifications and copied condition.csv into control.csv. I get this error, and I think it's telling me there is something wrong with the condition.csv file.

Step 1: Loading required libraries...
Step 2: Loading input data...
Step 3: Running the DE analysis...
Error in `$<-.data.frame`(`*tmp*`, "condition", value = integer(0)) : 
  replacement has 0 rows, data has 28
Calls: SalmonTE -> $<- -> $<-.data.frame
Execution halted

Both control.csv and condition.csv look like this:

SRR1111111_S1_L001_R2_001,condition
SRR2111111_S1_L001_R2_001,condition
SRR3111111_S1_L001_R2_001,control
SRR4111111_S1_L001_R2_001,control
SRR5111111_S1_L001_R2_001,control
SRR6111111_S1_L001_R2_001,condition
(...)
SRR2811111_S1_L001_R2_001,condition

Also, in the command line I specified --conditions=control,condition without whitespaces.

Do you have an idea for what is going wrong here?

Thank you

[hyunhwan-jeong]

Hi @nrius, there was an error on README.md (control.csv should be replaced as condition.csv, sorry for the confusion), and I have corrected it. Did you include SampleID,control to the first line of the file? It might not work if you didn't include the line in the file. And again, all the sample information has to be inside of `condition.csv'. If it does not solve your problem then, please send your EXPR.csv file.

Thank you,

Hyun-Hwan Jeong

[nrius]

Hi, The condition.csv file was ok, but it turns out the names of the fastqs were too long, I shortened them to 10 characters with only one underscore and it worked perfectly.

Thanks for your reply,

Nuria

[hyunhwan-jeong]

@nrius, I believe this was not supposed to happen, so can you share the name of files, EXPR.csv, and condition.csv to hyunhwaj@bcm.edu if you don't mind? It should be helpful to improve this tool.

Thank you,

Hyun-Hwan Jeong

[nrius]

Hi Hyun-Hwan Jeong Sure, in the attachment, you can find the initial EXPR and condition files (before the change name). Hope it helps.

Best,

Nuria

Nuria Rius Camps

El lun., 2 dic. 2019 a las 10:00, Hyun-Hwan Jeong (notifications@github.com) escribió:

@nrius https://github.com/nrius, I believe this was not supposed to happen, so can you share the name of files, EXPR.csv, and condition.csv to hyunhwaj@bcm.edu if you don't mind? It should be helpful to improve this tool.

Thank you,

Hyun-Hwan Jeong

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