User: mforde84

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mforde8410
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Posts by mforde84

<prev • 22 results • page 1 of 3 • next >
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Comment: C: pd.mirna.4.0 normalization to spike-in probesets
... It doesn't appear that subset is implemented yet: > normalize(bgd, "loess", subset=spikes$fid) Normalizing... ^C Warning message: In .local(object, ...) : Subset not implemented (yet). Returning everything. So my thought on getting around this would be to extract out the exprs from the backg ...
written 3 months ago by mforde8410
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Comment: C: pd.mirna.4.0 normalization to spike-in probesets
... Never mind, I see it in the documentation. ...
written 3 months ago by mforde8410
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Comment: C: pd.mirna.4.0 normalization to spike-in probesets
... One additional question that I presume you can help me with. How would you suggest doing the background correction without summarization? I tried using the bg.correct method in affy, however both the mas and rma options either produce an error or a segfault. I think it has to do with the design of t ...
written 3 months ago by mforde8410
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Comment: C: pd.mirna.4.0 normalization to spike-in probesets
... You're awesome. Thanks for the clarifications. ...
written 3 months ago by mforde8410
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pd.mirna.4.0 normalization to spike-in probesets
... Hello, I have CEL files from GeneChip miRNA v4.0. I would like to generate normalized data using a Loess curve subset with only spike-in probesets. Package affy has a function normalize.loess(mat, subset=...) which can accomplish the subsetting portion, however after importing the CEL data using th ...
microarry pd.mirna.4.0 written 3 months ago by mforde8410 • updated 3 months ago by James W. MacDonald45k
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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 9 months ago by mforde8410
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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 9 months ago by mforde8410 • updated 9 months ago by James W. MacDonald45k
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Comment: C: EGSEA - failing to write report
... Ahhh, ok let me try real quick. ...
written 9 months ago by mforde8410
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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 9 months ago by mforde8410
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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 9 months ago by mforde8410

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