User: federico.comoglio

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100
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Trusted
Location:
Switzerland
Last seen:
2 years, 2 months ago
Joined:
8 years, 6 months ago
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f****************@gmail.com

Posts by federico.comoglio

<prev • 31 results • page 3 of 4 • next >
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Comment: A: Rtracklayer not able to set session genome to mm9 using US server. hg19 and euro
... Likely related to what I describe here: https://support.bioconductor.org/p/67403/ Federico ...
written 4.4 years ago by federico.comoglio100
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Comment: C: Failed to set session genome to ...
... Hi Herve',  thanks for your message. The problem seems to be generalized, though. I get: > library(rtracklayer) > session <- browserSession() > genome(session) <- "dm6" Error in `genome<-`(`*tmp*`, value = "dm6") : Failed to set session genome to 'dm6' I'm running this code o ...
written 4.4 years ago by federico.comoglio100
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Comment: A: Failed to set session genome to ...
... I also tried to supply a different genome argument (e.g. hg19, mm9 or dm3) and I get the same error. ...
written 4.4 years ago by federico.comoglio100
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Failed to set session genome to ...
... Hi All, I just downloaded the latest GenomicFeatures, and noticed that although the Drosophila dm6 genome is within the output returned by ucscGenomes(), neither refGene, ensGene or flyBaseGene tables can be retrieved using: txdb <- makeTxDbFromUCSC( "dm6", tablename = "ensGene" ) Error in `ge ...
genomicfeatures maketxdbfromucsc written 4.4 years ago by federico.comoglio100 • updated 3.9 years ago by Michael Lawrence11k
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Answer: A: QC for Affymetrix miRNA 4.0 arrays: Error from qc/QCReport
... Hi Jim, thank you for your insightful answer. I do agree with you that QC such as RNA degration do not make sense for these arrays. However, spike-in controls should be meaningful. In addition, even a simple boxplot of raw intensity values fail in a call to  boxplot( rawData ) raising the same e ...
written 4.6 years ago by federico.comoglio100
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QC for Affymetrix miRNA 4.0 arrays: Error from qc/QCReport
... Hi, I'm analyzing >30 Affymetrix miRNA 4.0 microarrays. As the corresponding miRNA 4.0 CDF is not available from BioC, I downloaded it from the Affymetrix website. I then created a CDF environment using make.cdf.env (makecdfenv package) and read in the data as: rawData <- ReadAffy( ) rawDat ...
affy simpleaffy affyqcreport written 4.6 years ago by federico.comoglio100
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Answer: A: got an error with wavClusteR package; NSBS(i, x, exact = exact, upperBoundIsStri
... You're welcome, Hee. Please let me know should you need further support.  Best wishes, Federico ...
written 4.6 years ago by federico.comoglio100
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Answer: A: got an error with wavClusteR package; NSBS(i, x, exact = exact, upperBoundIsStri
... Hi Hee, thank you for pointing out this bug. This issue has been fixed very recently and I would suggest you download wavClusteR version 1.99.3 from my GitHub repository: https://github.com/FedericoComoglio/wavClusteR See http://federicocomoglio.github.io/wavClusteR/ for more information. The same ...
written 4.6 years ago by federico.comoglio100
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Answer: A: Vranges (somatic signature) VariantAnnotation
... Hi humaasif79, your problem is that the fl variable you defined is an empty string. if your goal is simply to build a VCF file, I found a different vcf file in the extdata directory of the package that you could read in using readVcf. Try: fl <- system.file('extdata', 'gl_chr1.vcf', package= ...
written 4.9 years ago by federico.comoglio100
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Bioconductor Digest, Vol 118, Issue 25
... Hi Wei, if you want to obtain the correlation between your vector, say v, and each of the columns of a matrix (M) you can simply use the cor function on the augmented matrix having your vector as first column and all the original columns of M following as [v M]. You then need to store only the firs ...
written 6.7 years ago by federico.comoglio100

Latest awards to federico.comoglio

Popular Question 2.2 years ago, created a question with more than 1,000 views. For QC for Affymetrix miRNA 4.0 arrays: Error from qc/QCReport
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Failed to set session genome to ...
Scholar 3.4 years ago, created an answer that has been accepted. For A: got an error with wavClusteR package; NSBS(i, x, exact = exact, upperBoundIsStri
Scholar 4.6 years ago, created an answer that has been accepted. For A: got an error with wavClusteR package; NSBS(i, x, exact = exact, upperBoundIsStri

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