User: 刘鹏飞

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刘鹏飞80
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Posts by 刘鹏飞

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Comment: C: How does pathview deal with enzyme with several coding genes?
... Thank you for your comprehensive explanation£¬I read some parts of the vignette in details as you mentioned, realized several ways to visualize my data. Pathview is really a nice tools£¡ I also found a little problem, although it does not affect my use. when the list of expression data has only one ...
written 3.7 years ago by 刘鹏飞80
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Answer: A: How does pathview deal with enzyme with several coding genes?
... Hi, I found in the mol.data that pathview just do some add calculation, for example, acs-1=-1.7283407; acs-2=-4.1076455, in the mol.data, just acs-1 was chosen, and data was set as acs-1=-5.835986205; but, for Gene Mtc_1383/aroF; Mtc_2501/fbaA; Mtc_0384/fbaB; Log2fc -1.22;-0.118;1.645; in mol.dat ...
written 3.8 years ago by 刘鹏飞80
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How does pathview deal with enzyme with several coding genes?
... Dear all, Now I am using pathview to map my RNAseq expression data to the keggmap of my organism 'mez'. I want to know how pathview deal with the colour of enzyme with several conding genes, for example: In pathway: Glycolysis / Gluconeogenesis, mez00010, the gene node (enzyme 4.1.2.13) has 3 gene ...
rnaseq organism pathview written 3.8 years ago by 刘鹏飞80
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goseq: pwf: Error in if (hi <= low) { : missing value where TRUE/FALSE needed
... Hi, all I am trying to use goseq for RNAseq data analysis of a non-native bacteria, I fetch the genelength data and GO term data by using ensembl Perl API. Differential expression was done by DESeq2. After data run pwf of goseq, error occurred as following: ### Error in if (hi <= low) { : mis ...
rnaseq go goseq deseq2 written 3.8 years ago by 刘鹏飞80
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help: goseq and makeOrgPackageFromNCBI in AnnotationForge
... Hi all and M. Carlson I am now working on an archaea, which is not a common organism. I want to use goseq to do the GO analysis of my RNAseq data.In order to creat the category mappings(relationship between GO and gene id), I try to use the makeOrgPackagesFromNCBI.Now the problem comes as followin ...
rnaseq go organism annotationdbi goseq written 4.0 years ago by 刘鹏飞80 • updated 4.0 years ago by Marc Carlson7.2k
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makeTranscriptDbFromGFF fails on NCBI Bacteria genomes
... Hi, Now I am want to use goseq for doing GO analysis of my bacteria RNA- seq data, but now I am stucked by the following issue: 1, makeTranscriptDbFromGFF First download gff from NCBI( ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Pelotomaculum_thermopropio nicum_SI_uid58877/NC_009454.gff), try to use ...
go transcriptdb goseq genomes written 4.1 years ago by 刘鹏飞80 • updated 4.1 years ago by Marc Carlson7.2k
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Comment: C: Install DESeq2 on windows R 3.0.1/2
... Hi£¬ Thanks Steve. I am not familiar with R and did not keep the sessionInfo() as the error appeared. And I think now the problem is solved by using Rtools to install package locfit from sources. >Can you explain what you mean by "automatically install"? Are you installing using the biocLite fun ...
written 4.1 years ago by 刘鹏飞80
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Install DESeq2 on windows R 3.0.1/2
... Hi I have a problem on installation of DESeq2 on windows. I use R 3.0.1. After automatically install, I loaded DESeq2, the error message: the package locfit is built before 3.0.0, you should reinstall it. I search the CRAN (http://ftp.ctex.org/mirrors/CRAN/), but the lattest version was built o ...
deseq2 written 4.1 years ago by 刘鹏飞80 • updated 4.1 years ago by Steve Lianoglou12k

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