User: Xiaokuan Wei

gravatar for Xiaokuan Wei
Xiaokuan Wei230
Reputation:
230
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Trusted
Location:
United States
Last seen:
1 year, 3 months ago
Joined:
7 years, 6 months ago
Email:
w**********@yahoo.com

Posts by Xiaokuan Wei

<prev • 32 results • page 1 of 4 • next >
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Comment: C: WGCNA maxBlockSize limit
... Got it, thank you Peter. ...
written 16 months ago by Xiaokuan Wei230
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WGCNA maxBlockSize limit
... Recently I ran a WGCNA network construction analysis. The array type has more than 50K genes but luckily I have a powerful cluster which has more than 600G memory, so I set the maxBlockSize=60000. But I got the error message: 'maxBlockSize must be less than 46340. Please decrease it and try again.' ...
microarray wgcna written 16 months ago by Xiaokuan Wei230 • updated 16 months ago by Peter Langfelder1.3k
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Comment: C: Does the BAM need to be sorted by name for "summarizeOverlaps" of "GenomicAlignm
... Thank you Valerie! That's very clear! -X ...
written 2.3 years ago by Xiaokuan Wei230
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Comment: C: Does the BAM need to be sorted by name for "summarizeOverlaps" of "GenomicAlignm
... Valerie, Thank you for your prompt response. It's good to know that we don't need to sort the BAMs. As I cannot find such information and finally it is clear. But out of curiosity, I assume that if I sort the BAM by name, will it increase the speed for "summarizeOverlaps". If I understand it right ...
written 2.3 years ago by Xiaokuan Wei230
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Does the BAM need to be sorted by name for "summarizeOverlaps" of "GenomicAlignments"
... Hi, I performed RNA-Seq using DESeq2 pipeline. When I tried to create count matrix I used "summarizeOverlaps" of "GenomicAlignments". I always sort BAM by name before this step. But I am now wondering if it's necessary as I haven't see any instruction on this part. I did ask the similar question on ...
rnaseq deseq2 genomicalignments written 2.3 years ago by Xiaokuan Wei230 • updated 2.3 years ago by Valerie Obenchain ♦♦ 6.4k
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Comment: C: GenomicFeatures error: rsqlite_query_send: could not execute1: database or disk
... Herve, Thank you for your answer and I am sorry that I cannot reply to you earlier. Actually, I don't think it's a memory issue as our server on cluster has a lot of memory. Also, I have to do this step to create trxDB using my laptop since I cannot do it using the server. It works fine without any ...
written 2.3 years ago by Xiaokuan Wei230
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GenomicFeatures error: rsqlite_query_send: could not execute1: database or disk is full
... Guys, I tried to use "GenomicFeatures" to create trxDb. But I kept hitting the same error as below. Actually, I have plenty of disk space and I really don't know how to solve this issue. Thank you for your any help!     hse<-makeTxDbFromGFF("/genome/human/hg19_ensemble.gtf",format="gtf") Prep ...
rnaseq genomicfeatures deseq2 written 2.4 years ago by Xiaokuan Wei230
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Comment: C: DESeq2: which normalized data matrix should I take?
... Got it, I think so. Thank you Michael. -W ...
written 2.7 years ago by Xiaokuan Wei230
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Answer: A: DESeq2: which normalized data matrix should I take?
... Ryan, Michael: Thank you for your informative answers to my question. I just have another question regarding this process. As to my understanding, the fold changes obtained from DESeq() is using raw counts instead of normalized one (rlog or vsn). So, if I extracted normalized matrix then do the f ...
written 2.7 years ago by Xiaokuan Wei230
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DESeq2: which normalized data matrix should I take?
... Hi,   I want to extract the normalized the data matrix (reads matrix) to do differential gene expression analysis by myself instead of using wald test the package provided as I don't have replicates in each comparison group. so, there is no statistical calculation but only fold change between two ...
deseq2 written 2.7 years ago by Xiaokuan Wei230

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Popular Question 2.3 years ago, created a question with more than 1,000 views. For DESeq2: which normalized data matrix should I take?

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