User: John

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John30
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1 year, 1 month ago
Joined:
3 years, 4 months ago
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t************@yahoo.com

Posts by John

<prev • 35 results • page 1 of 4 • next >
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Comment: C: CPM filtering in deseq2
... Thanks. I will do that :-) J. ...
written 3.3 years ago by John30
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Comment: C: CPM filtering in deseq2
... Hi Michael, Thank you so much. J. ...
written 3.3 years ago by John30
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Answer: A: CPM filtering in deseq2
... Thank you Steve. I will use fpm instead. Can I say dds[rowSums(fpm(dds)>1)>=2] in DESeq2 is similar to rowSums(cpm(counts)>1)>=2 in EdgeR filtering?  ...
written 3.3 years ago by John30
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Answer: A: CPM filtering in deseq2
... Thank you Michael. You are still using the read counts for filtering, right? I was looking for solution like rowSums(cpm(counts)>1)>=2. Does DESeq2 calculates cpm? I couldn't find in documentation. I can see that EdgeR does this.  Thank you for the help.  J. ...
written 3.3 years ago by John30
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CPM filtering in deseq2
... Hi, I know that DEseq2 can do low counts filtering but I wanted to set my threshold based on CPM values rather than count values then do filtering. Is there a way in DEseq2? Thanks for the help. J. ...
deseq2 written 3.3 years ago by John30
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Answer: A: R crash when matrix nrows exceeds 45000 using pheatmap/heatmap.2
... Thank you Raivo.  J. ...
written 3.3 years ago by John30
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R crash when matrix nrows exceeds 45000 using pheatmap/heatmap.2
... Hi, pheatmap(FW_SD, cluster_rows = T, cluster_cols = F, main = 'FW') > nrow(FW_SD) [1] 53049 R crashes. Is there hardcoded memory limitation? I have over 500GB RAM in my host. > sessionInfo() R version 3.2.3 (2015-12-10) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10 ...
heatmap.2 pheatmap written 3.3 years ago by John30
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Answer: A: Multiple condition analysis
... Thanks a lot Michael. ...
written 3.3 years ago by John30
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Answer: A: Multiple condition analysis
... Hi Michael, I have read the documents did the following. ddsHTSeq<-DESeqDataSetFromHTSeqCount(sampleTable=sampleTable, directory=INDIR, design=~time + daylength + salinity) dds <- DESeq(ddsHTSeq,betaPrior=FALSE, test="LRT", full=~time + daylength + salinity, reduced=~daylength) Now I have p ...
written 3.3 years ago by John30
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Answer: A: Missing data in replication
... Thanks Michael. I really appreciate your help.  ...
written 3.3 years ago by John30

Latest awards to John

Popular Question 13 months ago, created a question with more than 1,000 views. For CPM filtering in deseq2
Popular Question 13 months ago, created a question with more than 1,000 views. For DESeq heatmap based on threshold
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Converting first column to rownames
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Converting first column to rownames
Great Question 2.6 years ago, created a question with more than 5,000 views. For Converting first column to rownames
Popular Question 2.6 years ago, created a question with more than 1,000 views. For CPM filtering in deseq2
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Adding text labels to PCA plot
Scholar 3.3 years ago, created an answer that has been accepted. For A: Showing average of replications on heatmap

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