User: rhart

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rhart0
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Posts by rhart

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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 4 months 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 4 months 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 4 months 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 5 months 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 5 months 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)$basepairs<-x method to work.  So now I'll go back and re-create my original dds object--perhaps I screwed it up with my other trial methods.  But thanks--this seems to have solved my problem!   ...
written 5 months ago by rhart0
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Comment: C: Add avgTxLength to DESeqDataSet
... Nope, neither worked.  I'm working at the transcript level and I have the length for each transcript (calculated with a simple script from the gtf).  So tlen is a data frame with transcript_id's as row names and one column of data labeled "Len".  txOrder is a character array with the transcript_id ...
written 5 months ago by rhart0
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Answer: A: Add avgTxLength to DESeqDataSet
... (deleted)   ...
written 5 months ago by rhart0
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Add avgTxLength to DESeqDataSet
... I'd like to manually add a vector of transcript sizes to my DDS object.  I tried setting: dds@assays$data$avgTxLength=data.frame(row.names=txOrder,"avgTxLength"=tlen[txOrder,]) Where txOrder is the row names from the dds data and tlen is the (out of order) transcript list for those row names.  Th ...
deseq2 fpkm written 5 months ago by rhart0

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