User: kgorczak

gravatar for kgorczak
kgorczak10
Reputation:
10
Status:
New User
Location:
Belgium
Last seen:
3 days, 2 hours ago
Joined:
2 years, 3 months ago
Email:
k*******@up.poznan.pl

Posts by kgorczak

<prev • 10 results • page 1 of 1 • next >
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limma model including duplicated probes
... I have a microarray data with many duplicated probe names (some are duplicated 2 times, some 10 times, some 35 times). The package limma offers a function avereps() to average expression across the same probe names, e.g. y.ave <- avereps(y, ID=y$genes$ProbeName). However, I do not want to run lmF ...
limma written 10 weeks ago by kgorczak10
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Comment: C: Problem with summarizeOverlaps function
... Thank you a lot! if it's necessary, here is my e-mail: kgorczak@up.poznan.pl  ...
written 2.2 years ago by kgorczak10
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Comment: C: Problem with summarizeOverlaps function
... I sent to you a link to dropbox (by accident maybe even twice). And here is the code I use: library("Rsamtools") bamfiles <- BamFileList("accepted_hits.bam") seqinfo(bamfiles) library("GenomicFeatures") txdb <- makeTxDbFromGFF("exon_havana.gtf", format="gtf", circ_seqs=character()) columns ...
written 2.2 years ago by kgorczak10
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Comment: C: Problem with summarizeOverlaps function
... I even checked your profile ;-) but unfortunately I can see there only star signs instead of your email. Anyway, thank you and you will get my invitation to dropbox soon  ...
written 2.2 years ago by kgorczak10
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Comment: C: Problem with summarizeOverlaps function
... Is it possible to get your e-mail? I will send you a link to my data on dropbox. Thank you. ...
written 2.2 years ago by kgorczak10
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Comment: C: Problem with summarizeOverlaps function
... I followed your ideas: 1. I didn’t load the BiocParallel package. I got the same error: error 'validObject(.Object)': invalid class “SummarizedExperiment” object: 'rowRanges' length differs from 'assays' nrow 2. I selected chromosomes on the GRangesList object: library("Rsamtools") bamfile < ...
written 2.2 years ago by kgorczak10
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Problem with summarizeOverlaps function
... I am following RNA-seq workflow (http://www.bioconductor.org/help/workflows/rnaseqGene/) using my data and I am trying to get read counts using summarizeOverlaps function. Unfortunately, it is impossible because of this error:  error 'validObject(.Object)': invalid class “SummarizedExperiment” obje ...
genomicalignments read counting written 2.2 years ago by kgorczak10
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Comment: C: problem using makeTxDbFromGFF and exonsBy() functions
... I installed a new version of R and reinstalled 'GenomicFeatures' and now everything works fine. Thank you. ...
written 2.3 years ago by kgorczak10
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Comment: C: problem using makeTxDbFromGFF and exonsBy() functions
... I checked and it is ‘1.18.7’, but why if I installed it few hours ago using  source("http://bioconductor.org/biocLite.R") biocLite("GenomicFeatures") Output from sessionInfo() R version 3.1.2 (2014-10-31) Platform: x86_64-pc-linux-gnu (64-bit) locale:  [1] LC_CTYPE=pl_PL.UTF-8       LC_NUMERIC= ...
written 2.3 years ago by kgorczak10
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problem using makeTxDbFromGFF and exonsBy() functions
... I installed new package and added library GenomicFeatures. One of the changes in version 1.20 is renamed function makeTranscriptDbFromGFF() to makeTxDbFromGFF(), but using this new name I got an error that function cannot be found. Can you tell me why? (Btw, old function works fine) I follow with R ...
annotation genomicfeatures written 2.3 years ago by kgorczak10 • updated 2.3 years ago by Julian Gehring1.3k

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