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thelovelab / tximport

Transcript quantification import for modular pipelines
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Error in importing RSEM gene level result files #33

Closed Duanzpwt closed 5 years ago

Duanzpwt commented 5 years ago

I used this line of code to import RSEM ".gene.results" files: txi.rsem <- tximport(files, type = "rsem", txIn = FALSE, txOut = FALSE)，and it returns error："all(c(geneIdCol, abundanceCol, lengthCol) %in% names(raw)) is not TRUE" ， then i explicitly define the column names like in the line of code below： txi.rsem <- tximport("ceshi2.tsv", type = "rsem", txIn = FALSE, txOut = FALSE, tx2gene = NULL, countsFromAbundance = "no", varReduce = FALSE, dropInfReps = FALSE, ignoreTxVersion = FALSE, geneIdCol = "gene_id", txIdCol = "transcript_id", abundanceCol = "TPM", countsCol = "expected_count", lengthCol = "effective_length") it returns the same error. my files are just like the picture : QQ截图20190617121153

dfv commented 7 hours ago

Hi Duanzpwt,

Is it possible to know how the above error got solved ?

I am also experiencing the same error like below:

Error in tximport(files, type = "salmon", tx2gene = tx2gene, importer = my_read_tsv, : all(c(abundanceCol, countsCol, lengthCol) %in% names(raw)) is not TRUE

Thanks