User: Yisong Zhen

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Yisong Zhen200
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Posts by Yisong Zhen

<prev • 23 results • page 1 of 3 • next >
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Answer: A: Failed to install 'DOSE' package. Win10, 'single candle'
... @Martin. Thanks. This problem has been sovled. I down-versioned the base R for Window. 'DOSE' installation in the R 3.3.3  also failed. And installation in R 3.3.2 was OK and I got the 'DOSE' package installed. ...
written 4 months ago by Yisong Zhen200
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Failed to install 'DOSE' package. Win10, 'single candle'
... source("https://bioconductor.org/biocLite.R") biocLite("DOSE") library(DOSE) Error: package or namespace load failed for DOSE?in readRDS(nsInfoFilePath): unknown input format ## This is the error message. I tried the debuger protocols, here and here: But not succeeded in installing it after usin ...
dose package installation windows10 written 4 months ago by Yisong Zhen200
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Comment: A: Install Rsubread in win10, failed, how to proceed?
... Thanks, @Gordon & @Martin. I tried to downsample my rawdata and use the same code to process them at the server side. This seems to be a dead-end. ...
written 4 months ago by Yisong Zhen200
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Install Rsubread in win10, failed, how to proceed?
... Dear Bioconductor users, Following is the error message, and I think the rsubread uses the sys/ioctl.h. But the current Rtools failed to find the corresponding library in its compling tool. Do I need extra step to provide any location information to C library? Any suggestions are apprecaited. My ...
rsubread windows10 rtools written 4 months ago by Yisong Zhen200 • updated 4 months ago by Wei Shi2.7k
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How to save the result from calling matchPWM?
... Dear Users, I called the matchPWM method in Biostrings package. The return object is XStringViews and I want to save the "hit" result in a file. It seemed that once there was a method named write.XStringViews, but I searched and found no corresponding information, maybe it already deprecated and no ...
biostrings written 4.0 years ago by Yisong Zhen200 • updated 4.0 years ago by Hervé Pagès ♦♦ 13k
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Comment: C: How can I extract promoter regions from a list NCBI genbank acc?
... Dear Marc, I read your code, It looks like that there is a misunderstanding. I did not clarify my question. In gene annotation from NCBI, same EntrezGene ID probably will have several 5 UTR-differentent ReSeq IDs. Then they will not share same promoter. What I want to do is to use the unique RefSe ...
written 5.0 years ago by Yisong Zhen200
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How can I extract promoter regions from a list NCBI genbank acc?
... Dear All, I read the GenomicFeatures manual, there is only a example to extract promoters from a list EntrezGeneID. So how can I extract a group promoters from a list NCBI genbank acc, like "NM_144551" "NM_019413""? I have already installed locally "TxDb.Mmusculus.UCSC.mm9.knownGene". Thanks. Y ...
genomicfeatures written 5.0 years ago by Yisong Zhen200 • updated 5.0 years ago by Marc Carlson7.2k
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probe ID<-> accession number
... Dear All, I use the following code to generate HTML report on deferential expression genes after LIMMA analysis. The code is from Bioinformatics and Computational Biology Solutions Using R and Bioconductor. Now, I want to add a column in the final output, which includes the gene accession number ...
probe limma written 7.3 years ago by Yisong Zhen200 • updated 7.3 years ago by James W. MacDonald45k
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batch effect
... Dear *Bioconductor* users, Is there some package besides ComBat to deal with batch effects? YiSong -- //-------------------------------------------------------------------- ------------------- // We have a hunger of the mind which asks for knowledge // of all around us, and the more we gain, ...
written 7.5 years ago by Yisong Zhen200 • updated 7.5 years ago by Wolfgang Huber13k
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normalization
... Dear BioC users, How could I compare the different arrays from different species? For example, supposed that we have array A from specie A (kidney) and array B from specie B(kidney). since they are from same tissue, we assume that most of them have same expression pattern. But kidney A and kidne ...
kidney written 7.6 years ago by Yisong Zhen200

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