User: mforde84

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mforde840
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Posts by mforde84

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Comment: C: Alternate expression of splice isoforms on Affy Clariom D assay
... Thank you for the useful clarification on the annotation packages. If you don't mind I have a couple follow up questions. I believe the array in question also has exon-intron JUC probes. Would diffSplice in the limma package only work for quantification of exon-exon junctions from PSR probes, or wou ...
written 6 weeks ago by mforde840
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Alternate expression of splice isoforms on Affy Clariom D assay
... Hello, I have a quick question concerning the analysis of the Affy Clariom D chip, where we are interested in quantifying splice isoforms (e.g., exon skipping, intron retention, alternate 3', alternate 5' events). I've worked with gene-level analyses previously, but not transcript so I assume there ...
affy differential expression alternate expression written 6 weeks ago by mforde840 • updated 6 weeks ago by James W. MacDonald42k
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Comment: C: EGSEA - failing to write report
... Ahhh, ok let me try real quick. ...
written 7 weeks ago by mforde840
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Comment: C: EGSEA - failing to write report
... Removing the forward slash doesn't help either. > contrasts <- makeContrasts( + groups1-(groups2+groups3), + groups2-(groups1+groups3), + groups3-(groups1+groups2), levels=group.contrasts) > gsa <- egsea(voom.results=dge, + contrasts=contrasts, + gs.annots=gene_idx, + baseGSEAs=egs ...
written 7 weeks ago by mforde840
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Comment: C: EGSEA - failing to write report
... Yea, I figured this was the problem. However how do I remove the / from the contrast, without losing the contrast? e.g., grp1-(grp2+grp3) is not the same as grp1-(grp2+grp3)/2   ...
written 7 weeks ago by mforde840
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Comment: C: EGSEA - failing to write report
... I was thinking that maybe it has something to do with the contrasts I'm setting up (in bold). I'm going to trying forming the contrasts without white space and see if this helps. #pipeline for RNAseq GSVA analysis ##install libraries #source("https://bioconductor.org/biocLite.R") #biocLite("GSVA" ...
written 7 weeks ago by mforde840
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EGSEA - failing to write report
... Hi, I'm having some difficulty with the ESGEA package. The esgea() command is unable to write it's report to disk. I've tried on three separate computers with and without sudoer privledges and I get the same error. > gsa <- egsea(voom.results=dge, + contrasts=contrasts, + gs.annots=gene_i ...
write egsea written 7 weeks ago by mforde840 • updated 7 weeks ago by Monther Alhamdoosh40
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Comment: C: Contrasts in GOexpress analysis?
... Hi Kevin, Thanks for the clarifications. I'll run some test tomorrow, and do some comparisons and see what looks suitable. Again, thanks for the nice response. Martin ...
written 9 weeks ago by mforde840
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Comment: C: Contrasts in GOexpress analysis?
... Thanks, Gordon. This is very helpful. ...
written 9 weeks ago by mforde840
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Contrasts in GOexpress analysis?
... Hi, I'm a little confused by what's actually going on with the analysis for this package. The main function can take a factor of any size and returns enriched GO terms and pval based upon those factors using random forest regressions. I'm having difficulty understanding what the returned pvalues ...
gene ontology goexpress written 9 weeks ago by mforde840 • updated 9 weeks ago by kevin.rue200

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