Differential Analysis with iCLIP results, Error in data[[rowvar]]

Pipelines Differential Expression Analysis
1

Dear Flow.Bio team,

I’m executing a Differential Analysis with iCLIP results, however I keep getting the same error. So the samplesheet is (after succeding in the SAMPLE_DIFF_SAMPLESHEET_CHECK step):

|sample_id|condition|
|Tamarillo_RepUV1|UV|
|Tamarillo_RepUV2|UV|
|Tamarillo_noUV1|noUV|

And the count file is a .tsv with this information (example of the first 6 lines):

GeneID Tamarillo_RepUV1 Tamarillo_RepUV2 Tamarillo_noUV1
PGSC0003DMG400000543 0.143235446 0.050160741 0.000564731
PGSC0003DMG400032159 0.104394383 0.046646655 0
PGSC0003DMG400028852 0.105188531 0.046306582 0.000847096
PGSC0003DMG400007288 0.109448053 0.039108374 0
PGSC0003DMG400006857 0.088294834 0.042792497 0

But, then, in the R_DESEQ2 I keep getting the following error:

Error in data[[rowvar]] :
attempt to select less than one element in get1index
Calls: read_delim_flexible → read.delim → read.table
Execution halted

Can you help me understand what went wrong and how to fix this, please?

2

Hi Ricardo,

Happy new year! Please share the execution with me (username CharlotteC) so I can look in more detail - it seems like at some point R is trying to read an empty file. I suspect this is because you are working with plant data and in this pipeline the GSEA analysis doesn’t support plants, your gene IDs are very atypical. Ideally we would write an option to skip this for unsupported genomes. But yeah, if you share I can confirm my hunch.

Cheers,
Charlotte