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pachterlab / sleuth

Differential analysis of RNA-Seq
http://pachterlab.github.io/sleuth
GNU General Public License v3.0
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unable to export table from Shiny #242

Open VPankievicz opened 4 years ago

VPankievicz commented 4 years ago

Can you help me figure out why I'm not able to get any table from Shiny app.

The message showing is: " DataTables warning: table id=DataTables_Table_1 - Requested unknown parameter '4' for row 125. For more information about this error, please see http://datatables.net/tn/4" And then, all the data in the table is only random characters and numbers, I don't see the transcripts ids anymore, and no values.

Thank you

Daironbio commented 4 years ago

Please, if you find a solution for this issue, I´ll be glad to know. I´m having the same issue.

I´m using TAIR10 transcriptome for Arabidopsis as the index builder in Kallisto, and importing the three data files from Kallisto into RStudio/Sleuth. When I run the models and then "sleuth_live(so2)", the tables just don´t appear, having the same error message... Thank you in advance for your help!

biomaRt::listMarts(host = "plants.ensembl.org/")

mart1 <- biomaRt::useMart(biomart = "plants_mart", host = 'plants.ensembl.org/')

mart <- biomaRt::useMart(biomart = "plants_mart", dataset = "athaliana_eg_gene", host = 'plants.ensembl.org/')

t2g <- biomaRt::getBM(attributes = c("ensembl_transcript_id", "ensembl_gene_id", "description", "external_gene_name"), mart = mart)

t2g <- dplyr::rename(t2g, target_id = ensembl_transcript_id, ens_gene = ensembl_gene_id, ext_gene = external_gene_name)

so2 <- sleuth_prep(s2c, full_model = ~condition, target_mapping = t2g, aggregation_column = 'ens_gene', read_bootstrap_tpm=TRUE, extra_bootstrap_summary = TRUE)