User: rhart

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rhart0
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Posts by rhart

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Comment: C: windows tximport fail
... Thanks. h5lc() showed the contents of the file correctly. Working backwards from that I am now able to import on Windows without error. Don't know what changed or if there was an error in my files vector. In any case, problem solved and sorry to waste your time. ...
written 3 months ago by rhart0
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windows tximport fail
... I've been using tximport with output from Kallisto. After recent updates, including R to 3.6.1, I now get the following error on Windows: txi.kallisto=tximport(files,type="kallisto",txOut=T,ignoreTxVersion = T,countsFromAbundance = 'scaledTPM') Error in rhdf5::h5ls(h5File) : HDF5. Object ...
rhdf5 tximport written 3 months ago by rhart0 • updated 3 months ago by Michael Love26k
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Answer: A: Failure to load cufflinks data into cummeRbund
... Better: load the development version: http://bioconductor.org/packages/devel/bioc/html/cummeRbund.html   ...
written 2.2 years ago by rhart0
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Answer: A: Failure to load cufflinks data into cummeRbund
... These changes will solve the problem, all in "database-setup.R" in the source R folder:   Line 227 insert: names(diff)[10]="log2_fold_change"  #fix problem with importing col name Line 232 replace with: insert_SQL<-"INSERT INTO geneExpDiffData VALUES(:test_id,:sample_1,:sample_2,:status,:value ...
written 2.2 years ago by rhart0
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Comment: C: Failure to load cufflinks data into cummeRbund
... I've made progress with diagnostics.  The error is in the loadGenes() function as listed in the database-setup.R source file.  First, under the "Handle Samples Names" section, on line 152, make.db.names() is called.  This is deprecated and replaced with dbQuoteIdentifier() . If I use this function, ...
written 2.2 years ago by rhart0
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Comment: C: Failure to load cufflinks data into cummeRbund
... Also, here's the header and first line of genes.fpkm_tracking -- the file that seemed to generate the error: tracking_id    class_code    nearest_ref_id    gene_id    gene_short_name    tss_id    locus    length    coverage    Ctrl0_FPKM    Ctrl0_conf_lo    Ctrl0_conf_hi    Ctrl0_status    Case0_FP ...
written 2.2 years ago by rhart0
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Failure to load cufflinks data into cummeRbund
... I'm suddenly unable to load cufflinks data into cummerbund.  I get this output from the readCufflinks() function: Creating database I:/EpiCenter_ISI/Hart/coga/better/Hs/cuffHs/cuffData.db Reading Run Info File I:/EpiCenter_ISI/Hart/coga/better/Hs/cuffHs/run.info Writing runInfo Table Reading Read ...
cummerbund written 2.2 years ago by rhart0
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Comment: C: Add avgTxLength to DESeqDataSet
... In creating a subset example object, I can now get the mcols(dds)$basepairs<-x method to work.  So now I'll go back and re-create my original dds object--perhaps I screwed it up with my other trial methods.  But thanks--this seems to have solved my problem!   ...
written 2.3 years ago by rhart0
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Comment: C: Add avgTxLength to DESeqDataSet
... Nope, neither worked.  I'm working at the transcript level and I have the length for each transcript (calculated with a simple script from the gtf).  So tlen is a data frame with transcript_id's as row names and one column of data labeled "Len".  txOrder is a character array with the transcript_id ...
written 2.3 years ago by rhart0
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Answer: A: Add avgTxLength to DESeqDataSet
... (deleted)   ...
written 2.3 years ago by rhart0

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Popular Question 2.2 years ago, created a question with more than 1,000 views. For Add avgTxLength to DESeqDataSet

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