User: AB

gravatar for AB
AB70
Reputation:
70
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Trusted
Location:
United States
Last seen:
2 months, 2 weeks ago
Joined:
4 years, 2 months ago
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Posts by AB

<prev • 15 results • page 1 of 2 • next >
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Error: node stack overflow when trying to plot large dataset using Complexheatmap
... Hi, I have a massive dataset that I want to use to make a heatmap using the Complexheatmap package. However, I'm getting the following error Error: node stack overflow Error during wrapup: node stack overflow I am not at liberty to share my original dataset and hence here is a sample data ...
complexheatmap written 11 weeks ago by AB70 • updated 11 weeks ago by Zuguang Gu180
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Comment: C: Getting gene ID's from camera results
... That did work. Thank you very much. But is there anyway to do it without knowing the indices ? I have a shiny interface that loads up the precomputed camera results from an Rdata and I need the interface to display the gene list when each row is clicked on. I have the gene set and the camera result ...
written 3.6 years ago by AB70
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Getting gene ID's from camera results
... Hi, I have used camera (limma package) to do a gene set enrichment analysis with a gene set from MSigDB. I was wondering if there is any way I could use the results from camera to get the genes belonging to that list.                                                                                  ...
limma camera written 3.6 years ago by AB70 • updated 3.6 years ago by phil.chapman140
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Error in makeCountSet function in ChIPComp package
... Hi everyone, I have a small ChIP_Seq dataset with 6 samples (3  replicates each of WildType and Knockout). I wanted to do a differential binding analysis with ChipComp package. When i tried to execute the makeCountSet() function, it is giving me this error  Making peak list...... Error in (functi ...
chipseq chipcomp makecountset written 3.8 years ago by AB70
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Batch correction in DESeq2
... Hi Everyone, I am working on RNA-Seq data. I'm using DESeq2 for my analysis. I have 20 samples from 3 batches. I am testing for 2 conditions, cond1 and cond2. dds<-DESeqDataSetFromMatrix(countData=countTable3,colData=coldata,design = ~cond1*cond2) When i performed PCA, I could clearly see some ...
rnaseq deseq2 combat removebatcheffect() batch effect written 4.0 years ago by AB70 • updated 3.5 years ago by adam0
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Comment: C: Converting annotation from UCSC to Ensembl
... Worked. Thank you very much.  ...
written 4.0 years ago by AB70
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Converting annotation from UCSC to Ensembl
... Hi everybody, I am doing differential gene expression analysis on 22 samples from 3 batches. I have the count matrix generated using summarizeOverlaps() function. The reference genome is mm10 from UCSC. I need the annotation in Ensemble to compare my results with the results from another person usi ...
annotation ensembl ucsc written 4.0 years ago by AB70 • updated 4.0 years ago by James W. MacDonald52k
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Comment: C: Estimating and removing batch effects from rna-seq dataset
... Thank you Dr.Lianoglu. I tried to implement sva but I am getting this error. Error in dat %*% (Id - mod %*% solve(t(mod) %*% mod) %*% t(mod)) :    requires numeric/complex matrix/vector arguments. this is my code data <- read.csv("data.csv") batch<-factor(c("b1","b1","b1","b1","b1","b1","b1 ...
written 4.2 years ago by AB70
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Estimating and removing batch effects from rna-seq dataset
... Hi everyone, I'm working on RNA-Seq datasets containing 22 samples from 3 batches. I used mm10 as the reference genome and generated the count table from the BAM files using GenomicAlignments package and then used the rpkm() function to get the rpkm data. Now I want to perform batch correction usin ...
rnaseq limma sva removebatcheffect() batch effect written 4.2 years ago by AB70 • updated 4.2 years ago by Jeff Leek580
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Comment: C: Finding gene lengths of mm10 to calculate rpkm grom count matrix of rna-seq data
... I used the summarizeOverlaps function from the GenomicAlignmnets package to get the count table ...
written 4.2 years ago by AB70

Latest awards to AB

Appreciated 17 months ago, created a post with more than 5 votes. For Batch correction in DESeq2
Popular Question 17 months ago, created a question with more than 1,000 views. For Finding gene lengths of mm10 to calculate rpkm from count matrix of rna-seq dataset
Epic Question 17 months ago, created a question with more than 10,000 views. For Batch correction in DESeq2
Student 17 months ago, asked a question with at least 3 up-votes. For Batch correction in DESeq2
Good Question 17 months ago, asked a question that was upvoted at least 5 times. For Batch correction in DESeq2
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Using RPKM data in bioconductor for gene expression analysis
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Finding gene lengths of mm10 to calculate rpkm from count matrix of rna-seq dataset
Great Question 2.7 years ago, created a question with more than 5,000 views. For Batch correction in DESeq2
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Batch correction in DESeq2
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Batch correction in DESeq2

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