User: shirley zhang

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shirley zhang1.0k
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Posts by shirley zhang

<prev • 102 results • page 1 of 11 • next >
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Steps of removing batch effects and hidden variables
... Dear List, For high-throughput experiments (mircroarray, RNASeq, etc) with many batches of samples, as a routine procedure, we are suggested to apply Combat, SVA, PCA or PEER method to remove batch effects and hidden variables before any downstream analysis. But in terms of specific steps, I have l ...
rnaseq normalization sva written 5.4 years ago by shirley zhang1.0k • updated 5.4 years ago by Lucia Peixoto330
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compare RNASeq with Exon array data at the gene-level and exon-level
... Dear List, I have 50 RNA samples and each sample has the following expression data: 1. Illumina RNAseq 75bp paired-end data 2. Affymetrix Human Exon 1.0 ST array My goal is to compare RNASeq with Exon array data at the gene-level and exon-level. To be fair, I was suggested to gene ...
rnaseq annotation written 5.4 years ago by shirley zhang1.0k
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Comment: C: SCAN.UPC for microarray and RNAseq data
... Thanks Steve. I will give your suggestion a try. Shirley On Fri, Jun 27, 2014 at 9:26 AM, Steve Piccolo wrote: > Yes, unless you want to compare directly against the exon array data. > > Having said that, if it would be a lot of work to convert your data to > RPKM, it might be wor ...
written 5.5 years ago by shirley zhang1.0k
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Comment: C: SCAN.UPC for microarray and RNAseq data
... If I need to convert my values to RPKM in order to be comparable/consistent with the public RNAseq RPKM values, then I could compare both RPKM values directly, not even bother to use UPC values. What do you think? Many thanks, Shirley On Fri, Jun 27, 2014 at 9:14 AM, Steve Piccolo wrote: > ...
written 5.5 years ago by shirley zhang1.0k
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Comment: C: SCAN.UPC for microarray and RNAseq data
... Hi Steve, Many thanks for your quick response. For RNAseq data, I have to compare my own RNAseq data with public RNAseq data which contains > 3000 samples. For this comparison, 1. I am planing to try UPC_RNASeq with read.counts as input for my own data. 2. However, the public large RNAseq data ...
written 5.5 years ago by shirley zhang1.0k
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SCAN.UPC for microarray and RNAseq data
... Dear Steve, I have a very large Affy Exon array data including >1000 samples, and I would like to compare them with RNAseq data. 1. In the SCAN..vignette.pdf, UPC_RNASeq can take read.counts matrix in which each row is for one gene, and each column for each sample. Is it possilbe for UPC taking ...
rnaseq affy written 5.5 years ago by shirley zhang1.0k • updated 5.5 years ago by Stephen Piccolo560
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Answer: A: ComBat:RT-PCR Data
... Dear Evan, I have a similar question for a long time. For different platform (rtPCR vs. high-throughput array/sequencing), the number of genes vs. the number of samples, which one is a more important issue for ComBat, for example, here are two data I have: 1. a rtPCR data with 100 genes, but 2000 ...
written 5.6 years ago by shirley zhang1.0k
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how to calculate gene length to be used in rpkm() in edgeR
... Dear List, I've been used edgeR for differential expression analysis for data generated from the same tissue, but different conditions. Now I have a RNAseq data A (n=20), and would like to compare them with another RNAseq data B (n=1,000 across different tissues). Since data B is normalized and ba ...
rnaseq edger rpkm written 5.6 years ago by shirley zhang1.0k • updated 5.1 years ago by Gordon Smyth39k
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Comment: C: Remove batch effect in small RNASeq study (SVA or others?)
... Thank you, Dr. Smyth. I really appreciate your constructive and thoughtful reply. Ryan, thank you too for your comments. Best, Shirley ...
written 5.6 years ago by shirley zhang1.0k • updated 4.9 years ago by Gordon Smyth39k
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Comment: C: Remove batch effect in small RNASeq study (SVA or others?)
... Dear Ryan, I think you are right. As shown by ?cpm ## S3 method for class 'DGEList' cpm(x, normalized.lib.sizes=TRUE, log=FALSE, prior.count=0.25, ...) BTW, do you have experience about how to set "prior.count", e.g. 0.25 vs. 5? Many thanks, Shirley ...
written 5.6 years ago by shirley zhang1.0k • updated 4.9 years ago by Gordon Smyth39k

Latest awards to shirley zhang

Epic Question 5.4 years ago, created a question with more than 10,000 views. For how to calculate gene length to be used in rpkm() in edgeR
Popular Question 5.4 years ago, created a question with more than 1,000 views. For missing value in plotDensity
Popular Question 5.4 years ago, created a question with more than 1,000 views. For Remove batch effect in small RNASeq study (SVA or others?)
Great Question 5.4 years ago, created a question with more than 5,000 views. For how to calculate gene length to be used in rpkm() in edgeR
Popular Question 5.4 years ago, created a question with more than 1,000 views. For Remove batch effect in small RNASeq study (SVA or others?)
Popular Question 5.4 years ago, created a question with more than 1,000 views. For how to calculate gene length to be used in rpkm() in edgeR
Popular Question 5.4 years ago, created a question with more than 1,000 views. For how to calculate gene length to be used in rpkm() in edgeR
Centurion 5.4 years ago, created 100 posts.

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