User: stephan.emmrich

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Posts by stephan.emmrich

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Comment: C: Using tximport on rsem files produces error while trying to read in files
... Ok, I will do that then. Thanks a lot for your help, very educating!! One thing about TPMs though: If I would want to compare between gene abundances in one sample-set vs another (e.g. one species vs the other), then I would choose TPMs, right? And log2 transform them for downstream DGE analysis. ...
written 6 months ago by stephan.emmrich0
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Comment: C: Using tximport on rsem files produces error while trying to read in files
... Ok, so here is an output i directly created by using our own sequenced data: gene_id transcript_id(s) length effective_length expected_count TPM FPKM gene:ENSG00000000003_TSPAN6 transcript:ENST00000373020_TSPAN6-201,transcript:ENST00000612152_TSPAN6-204,transc ...
written 6 months ago by stephan.emmrich0
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Comment: C: Using tximport on rsem files produces error while trying to read in files
... Interestingly, now I get Error: length(files) > 0 is not TRUE I read that this is a common issue with RSEM and shouldn't this in your script already take care of it? if (type == "rsem") { # protect against 0 bp length transcripts txi$length[txi$length < 1] <- 1 ...
written 6 months ago by stephan.emmrich0 • updated 6 months ago by Michael Love19k
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Comment: C: Using tximport on rsem files produces error while trying to read in files
... The files are from Blueprint DCC portal, primary analysis done by Grape2 pipeline (https://github.com/guigolab/grape-nf). This is the header and first 5 rows of such a file (total 30). gene_id transcript_id(s) length effective_length expected_count TPM FPKM posterior_ ...
written 6 months ago by stephan.emmrich0
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Comment: C: Using tximport on rsem files produces error while trying to read in files
... Great, that works! Now I have tximport 1.7.13. But sadly that gives me same error as from the original post with that commands: Error in if (is.null(importer) & !kallisto.h5) { :    missing value where TRUE/FALSE needed Weirdly, when I run a sample to try out tximport v.1.7.13: sTPM_hsa_T ...
written 6 months ago by stephan.emmrich0
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Comment: A: Using tximport on rsem files produces error while trying to read in files
... Thanks!   When I do this, then   > install_github(“mikelove/tximport”) Error: unexpected input in "install_github(“" I am using RStudio1.1.442 with R3.4.4 on a windows 7 PC, could windows be the problem here? ...
written 6 months ago by stephan.emmrich0
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Comment: A: Using tximport on rsem files produces error while trying to read in files
... I have 1.6. just downloaded today from Bioconductor ...
written 6 months ago by stephan.emmrich0
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Using tximport on rsem files produces error while trying to read in files
... Hi, I am trying to import RSEM output files into tximport. Using this code   sTPM_hsa <- tximport(files = rsem_files, type = "rsem", txIn = TRUE, txOut = FALSE, countsFromAbundance = "scaledTPM")   with   rsem_files <- list.files(sTPM_basedir, pattern = "genes", full.names = TRUE) rsem_ ...
rnaseq R tpm tximport rsem written 6 months ago by stephan.emmrich0

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