User: MatthewP

gravatar for MatthewP
MatthewP260
Reputation:
260
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Trusted
Location:
China
Last seen:
an hour ago
Joined:
1 year, 4 months ago
Email:
m***********@gmail.com

Posts by MatthewP

<prev • 101 results • page 1 of 11 • next >
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Comment: C: How to construct co-expression network with correlation matrix?
... Ok, I think [this post](https://www.biostars.org/p/285296/) is helpful for me. Thanks again! ...
written 3 days ago by MatthewP260
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Comment: C: How to construct co-expression network with correlation matrix?
... Thanks, Clément Frainay. I know `igraph` but I have the same confusion with you that is this the co-expression network? Many papers said use pearson correlation to construct such network, but no detail how to perform. As for me, I want to construct co-expression only for **differential expression ge ...
written 3 days ago by MatthewP260
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Comment: C: Gene expression correlation analysis
... Hey, can you also post your figure here? ...
written 4 days ago by MatthewP260
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How to construct co-expression network with correlation matrix?
... Hello, I know how to calculate pearson correlation matrix, but don't know how to construct co-expression network from it. Also shall I filter correlation matrix according each P value? Thanks! ...
rna-seq written 4 days ago by MatthewP260 • updated 2 days ago by Arindam Ghosh180
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Comment: C: It's there any GISTIC2.0 like tools?
... Sorry, I misunderstand function of `gistic`. I thought it's use to identify CNV from multiple samples, like some kind of merge many CNV results. ...
written 12 days ago by MatthewP260
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It's there any GISTIC2.0 like tools?
... `GISTIC2.0` can find CNV across a set of samples. I want to know it's there other tools can do the same thing? Thanks. ...
cnv written 12 days ago by MatthewP260 • updated 12 days ago by jared.andrews073.4k
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Answer: A: Transcript vs. Gene TPM counts?
... Hey, RNA-seq can output both gene and transcript read counts. TPM is normalized data, yes. ...
written 13 days ago by MatthewP260
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Comment: C: A question on GetPileupSummaries (GATK)
... Hey, I don't think you should use your `normal.vcf`. [Here](ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b151_GRCh38p7/VCF/) dbSNP site has `common_all_xxx.vcf.gz` , also I think GATK bundle will provide common variant file. ...
written 22 days ago by MatthewP260
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Comment: C: Mapping Entrez gene ids to Ensembl ids
... This is normal, many ENTREZ ID map to multiple ENSEMBL ID. ...
written 5 weeks ago by MatthewP260
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Comment: C: Principal Component Analysis PCA
... Hey, take DESeq2 as example, why use rlog instead of normalized read counts data? ...
written 5 weeks ago by MatthewP260

Latest awards to MatthewP

Centurion 3 days ago, created 100 posts.
Scholar 7 weeks ago, created an answer that has been accepted. For A: How to convert data from NCBI E-utilities.efetch to python data object?
Appreciated 3 months ago, created a post with more than 5 votes. For A: Problem with downloading GSE file by GEOquery
Scholar 3 months ago, created an answer that has been accepted. For A: How to convert data from NCBI E-utilities.efetch to python data object?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Problem with downloading GSE file by GEOquery
Scholar 9 months ago, created an answer that has been accepted. For A: How to convert data from NCBI E-utilities.efetch to python data object?
Supporter 9 months ago, voted at least 25 times.

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