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 22 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 22 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 22 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 22 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 22 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)$basepairs<-x method to work.  So now I'll go back and re-create my original dds object--perhaps I screwed it up with my other trial methods.  But thanks--this seems to have solved my problem!   ...
written 22 months ago by rhart0
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Comment: C: Add avgTxLength to DESeqDataSet
... Nope, neither worked.  I'm working at the transcript level and I have the length for each transcript (calculated with a simple script from the gtf).  So tlen is a data frame with transcript_id's as row names and one column of data labeled "Len".  txOrder is a character array with the transcript_id ...
written 22 months ago by rhart0
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Answer: A: Add avgTxLength to DESeqDataSet
... (deleted)   ...
written 22 months ago by rhart0
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Add avgTxLength to DESeqDataSet
... I'd like to manually add a vector of transcript sizes to my DDS object.  I tried setting: dds@assays$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 22 months ago by rhart0

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