User: Mike
Mike • 980
- Reputation:
- 980
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- Location:
- UK
- Last seen:
- 2 months, 3 weeks ago
- Joined:
- 2 years, 3 months ago
- Email:
- m***@gmail.com
Posts by Mike
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... Thanks Kevin, this is very useful code. ...
written 11 weeks ago by
Mike • 980
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... Hi All,
What are basic difference between Gene co-expression network and Gene regulatory network ? I want to build co-expression and regulatory network for a list of genes from RNAseq data, could you please suggest me tools for both type of networks.
Thanks ...
written 3 months ago by
Mike • 980
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1
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382
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1
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... Hi all,
I am using "findMotifs.pl" script from HOMER to find motifs from a list.
I used following command..
perl findMotifs.pl genelist.txt human motifoutputdir -len 25
I got following output list,
simple text file:
Motif Name Consensus P-value Log P-value q-value (Benjamini) ...
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... Thanks a lot, @cpad0112 ...
written 6 months ago by
Mike • 980
7
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1
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5 follow
1
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... Hi All,
Sorry for technical question.
I am trying to make a boxplot of gene expression data for some samples, and wanted to highlight specific points (expression value) based on gene name "TP53". I am able to highlight color in scatter plot but couldn't in boxplot, my code for scatter plot is
...
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... Thank you very much, Kevin ...
written 6 months ago by
Mike • 980
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2.2k
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... yes I installed vsn and loaded `library(vsn)`
then I check normalize.AffyBatch.vsn, but I couldnt get it...
?normalize.AffyBatch.vsn
normalize.AffyBatch.vsn package:vsn R Documentation
Wrapper for vsn to be used as a normalization method with expresso
Description:
W ...
written 6 months ago by
Mike • 980
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... Thank you Kevin, I got some errors in step1 data normalization
x <- expresso(
+ a,
+ bg.correct=FALSE,
+ normalize.method="vsn",
+ normalize.param=list(subsample=1000),
+ pmcorrect.method="pmonly",
+ summary.method="medianpolish"
+ )
normalization: v ...
written 6 months ago by
Mike • 980
1
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2
answers
823
views
2
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... Thank you Kevin for explanation. ...
written 6 months ago by
Mike • 980
0
votes
2
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823
views
2
answers
... Thank you Istvan for your help. ...
written 6 months ago by
Mike • 980
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