User: Johannes Rainer

gravatar for Johannes Rainer
Johannes Rainer1.3k
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Location:
Italy
Twitter:
@jotsetung
Last seen:
1 day, 19 hours ago
Joined:
4 years, 1 month ago
Email:
j**************@eurac.edu

PhD, Bioinformatics Group, Institute for Biomedicine, Eurac Research, Bolzano, Italy

 

Posts by Johannes Rainer

<prev • 258 results • page 2 of 26 • next >
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Comment: C: mitochodria isCircular equals to FALSE in EnsDb.Hsapiens.v86 and EnsDb.Mmusculus
... Thanks for pointing this out. I'll have to check the perl routines that fetch the data from the Ensembl databases. Something might be wrong there. I posted an issue at the ensembldb repo (https://github.com/jotsetung/ensembldb/issues/86)   ...
written 6 weeks ago by Johannes Rainer1.3k
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Comment: C: ensembldb salmon deseq2 txt2import right tool?
... You have to remove the transcript version number from the transcript IDs (i.e. the .1). Just be sure that the Ensembl version of the EnsDb you are using and the version that was used for kallisto match. A fast way to remove them is e.g. top_table$tx_id <- sub("\\.[0-9]*$", "", top_table$tx_id) ...
written 12 weeks ago by Johannes Rainer1.3k
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Comment: C: Intensity discrepancy between raw data and XCMS output
... Thanks for providing the commands you're using for the analysis. I can not tell if the parameters are correct for your data but using IPO is definitely a good starting point. However, as mentioned in my previous reply, you should use featureValues with value = "into" and not value = "index". As it i ...
written 3 months ago by Johannes Rainer1.3k
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Comment: C: Intensity discrepancy between raw data and XCMS output
... Without having a good understanding of your experimental setup and without looking into the actual data or seeing all commands with all parameters that you used it is pretty hard to tell what happens or where the problem is. Some suggestions: 1) do never use the default parameters, especially not f ...
written 3 months ago by Johannes Rainer1.3k
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Comment: C: Error 'names' attribute must be the same length as the vector xcms
... The thing with the missing fillPeaks is that fillPeaks just inserts 0 values if no signal could be filled-in while fillChromPeaks leaves them out (thus you'll get NA in this case - which in my opinion is the correct approach if something is missing). The reason why you still got the error is that yo ...
written 3 months ago by Johannes Rainer1.3k
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Comment: C: Error 'names' attribute must be the same length as the vector xcms
... To extract m/z from a certain file (e.g. the second one) you can use mz(filterFile(raw_data, 2)). Regarding the error you encounter. The Note says you have to set the sampclass using e.g. sampclass(xset) <- raw_data$sample_group, eventually you forget that? Also, the parameters of the diffreport ...
written 3 months ago by Johannes Rainer1.3k
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Comment: C: Error 'names' attribute must be the same length as the vector xcms
... Yes, the error means you are running out of memory. There is not much you can do apart from closing all other running applications and trying again. On the other hand, you don't need to extract the m/z values of all of your 50 files. I'd skip that as in the vignette it just illustrates how you can ...
written 3 months ago by Johannes Rainer1.3k
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Comment: C: Error 'names' attribute must be the same length as the vector xcms
... Dear Goh, can you please provide the output of sessionInfo()? The reason for the failure might be the warning that you got. This sounds like some problem with the parallel processing setup (something like a connection timeout if you used SnowParam/sock-based parallel processing). Try running the a ...
written 3 months ago by Johannes Rainer1.3k
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Comment: C: XCMS for GC-MS
... I don't have any GC-MS data examples, but I guess the processing is pretty much the same as for LC-MS, so you can use xcms for the processing. Have a look at the xcms vignettes for examples on the preprocessing. Eventually you could also have a look at https://github.com/jotsetung/metabolomics2018 t ...
written 4 months ago by Johannes Rainer1.3k
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Comment: C: Chromatographic peak detection failed for all files
... 1st, please re-install mzR using BiocInstaller::biocLite("mzR"). For the error, seems that proteowizard has problems reading this file. Can you please try the second part, i.e. with openMSfile and the backend = "Ramp" option? ...
written 5 months ago by Johannes Rainer1.3k

Latest awards to Johannes Rainer

Scholar 5 weeks ago, created an answer that has been accepted. For A: biomaRt package problem
Popular Question 5 weeks ago, created a question with more than 1,000 views. For reactome.db: reactome IDs not mapped to pathway names
Popular Question 5 weeks ago, created a question with more than 1,000 views. For How to get from xcmsRaw to a xcmsSet
Popular Question 5 weeks ago, created a question with more than 1,000 views. For Reading alignments above a mapq threshold from BAM files
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Plot data from VCF using Gviz?
Popular Question 3 months ago, created a question with more than 1,000 views. For Problem with biomart's listMarts function
Popular Question 6 months ago, created a question with more than 1,000 views. For reactome.db: reactome IDs not mapped to pathway names
Popular Question 6 months ago, created a question with more than 1,000 views. For Plot data from VCF using Gviz?
Scholar 17 months ago, created an answer that has been accepted. For A: How to map all Ensembl IDs to Gene Symbols- Problem with AnootationDbi
Scholar 17 months ago, created an answer that has been accepted. For A: Programatically download correct genome wide annotation package for given organi
Scholar 17 months ago, created an answer that has been accepted. For A: Is it possible to get Ensembl gene descriptions with ensembldb?
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Is it possible to annotated mitochondrial genes with ENSEMBL ids and Homo.sapien
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: How to map all Ensembl IDs to Gene Symbols- Problem with AnootationDbi
Appreciated 17 months ago, created a post with more than 5 votes. For A: How to map all Ensembl IDs to Gene Symbols- Problem with AnootationDbi
Appreciated 17 months ago, created a post with more than 5 votes. For A: makeTxDbFromBiomart Error: 1: Space required after the Public Identifier
Popular Question 17 months ago, created a question with more than 1,000 views. For Plot data from VCF using Gviz?
Popular Question 17 months ago, created a question with more than 1,000 views. For reactome.db: reactome IDs not mapped to pathway names
Guru 17 months ago, received more than 100 upvotes.
Voter 17 months ago, voted more than 100 times.
Scholar 17 months ago, created an answer that has been accepted. For A: Is it possible to annotated mitochondrial genes with ENSEMBL ids and Homo.sapien
Scholar 18 months ago, created an answer that has been accepted. For A: annotating gene for transcript type/biotype
Great Question 18 months ago, created a question with more than 5,000 views. For Problem with biomart's listMarts function
Student 19 months ago, asked a question with at least 3 up-votes. For Easy way to sort GRangesList by seqname/start position?
Student 20 months ago, asked a question with at least 3 up-votes. For Problem with biomart's listMarts function
Scholar 20 months ago, created an answer that has been accepted. For A: annotating gene for transcript type/biotype

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