search

thelovelab / tximeta

Transcript quantification import with automatic metadata detection
https://thelovelab.github.io/tximeta/
66 stars 11 forks source link

couldn't find matching transcriptome, returning un-ranged SummarizedExperiment #35

Closed sunliang3361 closed 4 years ago

sunliang3361 commented 4 years ago

Hi Mike, I used Mouse M24 transcript.fa from gencode at ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M24/gencode.vM24.transcripts.fa.gz, which was in your hash table https://github.com/mikelove/tximeta/blob/master/inst/extdata/hashtable.csv.

Do you know what my problem is? Thanks,

Liang

--

suppressPackageStartupMessages(library(SummarizedExperiment)) se <- tximeta(coldata) importing quantifications reading in files with read_tsv 1 2 3 4 5 6 7 8 9 10 11 12 couldn't find matching transcriptome, returning un-ranged SummarizedExperiment

mikelove commented 4 years ago

Usually this is because someone is using an older version of the package.

mikelove commented 4 years ago

For example, see #33

sunliang3361 commented 4 years ago

Thank you so much for your quick response. I solve this problem after updating tximeta version but have another error message. Can you give some hints?

y class: RangedSummarizedExperiment dim: 140948 6 metadata(6): tximetaInfo quantInfo ... txomeInfo txdbInfo assays(3): counts abundance length rownames(140948): ENSMUST00000193812.1 ENSMUST00000082908.1 ... ENSMUST00000082422.1 ENSMUST00000082423.1 rowData names(3): tx_id gene_id tx_name colnames(6): A1 A2 ... D2 D3 colData names(3): names condition type y$condition [1] "adequate" "adequate" "adequate" "deficient" "deficient" "deficient" y$type [1] "Female" "Female" "Female" "Female" "Female" "Female" y <- scaleInfReps(y) Error in infRepError(infRepIdx) : there are no inferential replicates in the assays of 'y'

mikelove commented 4 years ago

Can we continue with any follow ups on the support site? I’m going to mark this tximeta issue as closed.

If you are trying to use fishpond, note the fishpond vignette details about generating inferential replicates.