User: xfwang

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xfwang20
Reputation:
20
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New User
Location:
United States
Last seen:
3 years, 5 months ago
Joined:
4 years, 11 months ago
Email:
x*****@ku.edu

Posts by xfwang

<prev • 19 results • page 1 of 2 • next >
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Answer: A: RIPSeeker error Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.a
... Just in case people got same issue as mine: The issue is that it has to be “NULL” for option “strandType”, if it is non-strand specific sequencing. If use “*”, the error happens. ...
written 3.5 years ago by xfwang20
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RIPSeeker error Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) : subscript contains NAs or out-of-bounds indices
... Dear RIPSeeker people,  Since I did not get any response for added-comment to my previous question, I open this error as new question. Actually, I tried to dig into this error by different version of genome build, different version of tophat, and upgrading the bioconductor package. But, the error i ...
ripseeker written 3.8 years ago by xfwang20
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Comment: C: an annotation error when using RIPSeeker
... Sorry, this is not an answer. ...
written 3.8 years ago by xfwang20
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Answer: A: an annotation error when using RIPSeeker
... Dear Yue, I guess my error might be cause by the version of genome build that I use. For tophat2 alignment, I used GRCh37 downloaded from genome. But, I found the default recent genome annotation in biomaRt is GRCh38, is't it? If want to use annotation for genome build of hg19, I think I have to ch ...
written 3.8 years ago by xfwang20
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Comment: C: an annotation error when using RIPSeeker
...   Hi Yue, Thanks for your reply! It totally make sense. Actually, for my real data, I used the ensembl build version GRCh37. So, I don't have this issue for my real experience. However, I got a couple of questions about RIPSeeker. First, how does it differentiate biological reps and technical rep ...
written 3.8 years ago by xfwang20
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an annotation error when using RIPSeeker
... Dear RIPSeeker people, I tried to make RIPSeeker work by testing the system data. But I got an error as below, which seems an error when using biomaRt. Actually, I checked the host of "dec2011.archive.ensembl.org", which is not down when I run the code. Here is the code that I used:  extdata.dir ...
biomart ripseeker written 3.8 years ago by xfwang20
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how does DESeq2 make the inference
...   Dear folks,     I got stuck about how DESeq2 get inference or calculated test_statistics for differential tests. There is a gene of my interest. I want to dot testing between 2 samples/conditions (no replicates) to see if it is significant differentially expressed. Here is the normalized count ...
deseq2 written 4.1 years ago by xfwang20 • updated 4.1 years ago by Michael Love26k
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Comment: C: DESeq2 input for PE data (Raw count-pairs or 2 x Raw count-pairs)
... Thanks a lot! ...
written 4.3 years ago by xfwang20
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DESeq2 input for PE data (Raw count-pairs or 2 x Raw count-pairs)
... Dear there, I know DESeq2 expects raw read counts as the inputs which is important for DESeq2's statistical model to hold (it has been emphasized many many times). For singed-end reads, the counts should be the number of reads mapped to the gene. But, how about paired-end data, is it the number of ...
deseq2 written 4.3 years ago by xfwang20 • updated 4.3 years ago by Ryan C. Thompson7.4k
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Answer: A: A couple of questions about baseMean, RPKM, and multi-factor analysis for DESeq2
... Hi Michael, I am sorry to bother you again.  I am trying to see what is going on by using LRT ( they might produce similar results). But I don't know how to express the reduced model for one factor analysis in DESeq2. If there is one treatment factor say 'trt', then the full model is "full=~trt" b ...
written 4.8 years ago by xfwang20

Latest awards to xfwang

Popular Question 3.5 years ago, created a question with more than 1,000 views. For A couple of questions about baseMean, RPKM, and multi-factor analysis for DESeq2
Popular Question 4.1 years ago, created a question with more than 1,000 views. For A couple of questions about baseMean, RPKM, and multi-factor analysis for DESeq2

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