User: bojingjia

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bojingjia10
Reputation:
10
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New User
Location:
United States
Last seen:
2 years, 2 months ago
Joined:
4 years, 1 month ago
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b********@gmail.com

Posts by bojingjia

<prev • 13 results • page 1 of 2 • next >
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DESeq2 Two-Factor Interaction Terms
... I am trying to understand the difference explored by interaction term for DESeq2. The vignette (p.38) explains that the interaction term answers: is the condition effect ***different*** across genotypes? There are two ways I think we can interpret this difference, and I'm wondering how to extract th ...
deseq2 rna-seq written 2.7 years ago by bojingjia10
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Comment: C: Supervised feature selection/clustering in R
... Hi Sean, Thanks for your response. I've been using DESeq2 for sometime now, and I'm not satisfied with the built-in clustering algorithms. To be more specific, DESeq2 clusters using pheatmaps, which looks at the samples (correct me if I'm wrong) blindly, and clusters them by sample distance. In the ...
written 3.6 years ago by bojingjia10
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Comment: C: Guided clustering using pheatmaps
... Sorry if I didn't make myself clear. I have been using DESeq2 to do differential gene expression, and the replicates don't cluster together. I'm wondering if there is a strategy to do supervised feature selection in DESeq2. ...
written 3.6 years ago by bojingjia10
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Supervised feature selection/clustering in R
... I have a couple sets of single-level RNA-seq experiments in which I'm identifying clusters of upregulated/downregulated genes across one treatment (ie. WT against KO). There are multiple biological replicates within each group - the problem is that there is in-group variance and the PCA shows that t ...
clustering pheatmaps deseq2 rna-seq written 3.6 years ago by bojingjia10
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htseq-count produces no features amid alignment
... I recently aligned some sequencing data using STAR against an mm10 prebuilt genome. Afterwards, I sorted and indexed using samtools, and proceeded to generate read counts using htseq-count (and appropriately, an mm10 Ensembl gtf file). But all of my read counts are peculiarly all 0's, classified as ...
htseq-count alignment samtools rna-seq myposts written 3.6 years ago by bojingjia10 • updated 2.1 years ago by Biostar ♦♦ 20
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Comment: C: HTSeq-count wrong reads count
... I am having the same problem, @ariesliu324, did you manage to resolve this issue? ...
written 3.6 years ago by bojingjia10
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Comment: C: Mapping mouse gene symbols to Entrez IDs in GAGE
... Thanks! That solved the errors. I am still unable to completely map all the gene symbols, do you have any suggestions? ...
written 3.8 years ago by bojingjia10
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Comment: C: Mapping mouse gene symbols to Entrez IDs in GAGE
... ## Load required libraries library("DESeq2") library("gage") library("pathview") ## Combine count files into dataframe # Import data from featureCounts countdata <- read.table("wt_CEvsRT.txt", header=TRUE, row.names=1) # Convert to matrix countdata <- as.matrix(countdata) head(countdata) # ...
written 3.8 years ago by bojingjia10
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Mapping mouse gene symbols to Entrez IDs in GAGE
... I've come across many posts about common errors using GAGE, and many of these common pitfalls relate to mismatching ID systems (Entrez gene ID, gene symbol, etc). I've read the "Gene set and data preparation" vignette, but still get errors when I try to convert my gene symbols to Entrez IDs. I have ...
gage deseq2 pathview gsea rna-seq written 3.8 years ago by bojingjia10 • updated 3.8 years ago by bigmawen310
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Comment: C: Is There Any Api Of Blast And Uniprot To Align Protein?
... @Neilfws, have you worked with UniProtJAPI before? I downloaded the API and tried to edit their example code, but I have trouble understanding how to run my edited projects. In the API, a .cmd file is given to execute the example files - compiling them on their own would result in errors. Please let ...
written 4.1 years ago by bojingjia10

Latest awards to bojingjia

Popular Question 2.5 years ago, created a question with more than 1,000 views. For Mapping mouse gene symbols to Entrez IDs in GAGE
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Supervised feature selection/clustering in R

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