User: shirley zhang
shirley zhang • 1.0k
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Posts by shirley zhang
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... 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 ...
written 5.1 years ago by
shirley zhang • 1.0k
• updated
5.1 years ago by
Lucia Peixoto • 330
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... 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 ...
written 5.1 years ago by
shirley zhang • 1.0k
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... 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 5.2 years ago by
shirley zhang • 1.0k
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... 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 5.2 years ago by
shirley zhang • 1.0k
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... 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 5.2 years ago by
shirley zhang • 1.0k
0
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1
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970
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1
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... 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 ...
written 5.2 years ago by
shirley zhang • 1.0k
• updated
5.2 years ago by
Stephen Piccolo • 560
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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 5.3 years ago by
shirley zhang • 1.0k
3
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10k
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... 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 ...
written 5.3 years ago by
shirley zhang • 1.0k
• updated
4.8 years ago by
Gordon Smyth ♦ 38k
0
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2
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5.0k
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... Thank you, Dr. Smyth. I really appreciate your constructive and thoughtful reply.
Ryan, thank you too for your comments.
Best,
Shirley
...
written 5.3 years ago by
shirley zhang • 1.0k
• updated
4.6 years ago by
Gordon Smyth ♦ 38k
0
votes
2
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5.0k
views
2
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... 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 5.3 years ago by
shirley zhang • 1.0k
• updated
4.6 years ago by
Gordon Smyth ♦ 38k
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For how to calculate gene length to be used in rpkm() in edgeR
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For Remove batch effect in small RNASeq study (SVA or others?)
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created a question with more than 1,000 views.
For how to calculate gene length to be used in rpkm() in edgeR
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For how to calculate gene length to be used in rpkm() in edgeR
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