User: LuisNagano

gravatar for LuisNagano
LuisNagano40
Reputation:
40
Status:
New User
Location:
University of Campinas
Last seen:
3 months, 3 weeks ago
Joined:
3 years, 7 months ago
Email:
n**********@gmail.com

Posts by LuisNagano

<prev • 24 results • page 1 of 3 • next >
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Comment: C: R package for pearson's correlation plot
... I already use Corrplot, but it's not that specific package that I want ...
written 3 months ago by LuisNagano40
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R package for pearson's correlation plot
... Which R package should I use to get a plot like this??? It's a Pearson's correlation analysis ![enter image description here][1] [1]: https://www.frontiersin.org/files/Articles/345188/fgene-09-00328-HTML/image_m/fgene-09-00328-g008.jpg ...
pearson package correlation R written 3 months ago by LuisNagano40
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Comment: C: p-value in Limma vs Graphpad
... Thank you very much, dsull! It was a great explanation. I want to plot a single gene in a bar plot using microarray data, because my resources here are scarce, then make perturbations and qPCR is not possible now. I want to use deposited data to see the expression of some targets of my interest ar ...
written 5 months ago by LuisNagano40
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p-value in Limma vs Graphpad
... Hello guys, I have some statistical issue. When I analyze my microarray data using RMA normalization, i get pvalue and adj-p from differential analysis. But when I go to graphpad to make analysis using the same normalized data, the result gives me a very different pvalue. I know that necessarily t ...
p-value adj p limma graphpad written 5 months ago by LuisNagano40 • updated 5 months ago by dsull1.0k
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Comment: C: How to make differential expression analysis with normalized data?
... The authors don't cite the tool used for normalization. DEseq2 only works with genes raw counts, doesn't it? I have normalized data in FPKM. I want a package for analyse any normalized expression data, like MAS5, RSEM, FPKM, TPM... ...
written 7 months ago by LuisNagano40
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How to make differential expression analysis with normalized data?
... Hello, could anyone help me out? Is there any R package that runs differential expression analysis or statistical test like generating log2FC and adj-p values from normalized RNA-seq and Array expression values? The available data that I need to analyze is in FPKM, a table with ~50000 genes, I don't ...
fpkm deg rna-seq written 7 months ago by LuisNagano40 • updated 7 months ago by ATpoint32k
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Pearson Correlation Issue
... I'd like to run a Pearson correlation for my gene of interest, for example, I would like to search within my normalized RNA-seq data, all genes with Pearson correlation greater than> 0.9 with my gene of interest. I ran this code dow but it runs all the genes against all the genes, after that I c ...
pearson correlation hmisc overload server written 13 months ago by LuisNagano40
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(Closed) How to convert chromosomal coordinates (Bedgraph) into gene symbols?
... Hi, processed data that I downloaded is in bedgraph format with chromosomal coordinates, but i need the gene symbols to make differential expression. I want to convert chromosomal coordinates into gene symbols or ensembl_ids, how i do that?! chr1 17434 17439 chr1 17439 17440 chr1 17440 ...
gene symbols bedgraph chromosomal coordinates bed written 13 months ago by LuisNagano40
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Comment: C: Transform Bedgraph counts into Gene Counts (DESeq2 input)
... Thank you, Gocougs, I guess that values are FPKM or RPM values, right?! but I want the gene symbols of that bedgraph files. How do I convert chromosomal coordinates into Gene Symbols/Ensembl_ids? chr1 17434 17439 chr1 17439 17440 chr1 17440 17443 The GSE number is GSE118530 ...
written 13 months ago by LuisNagano40
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Transform Bedgraph counts into Gene Counts (DESeq2 input)
... Hello guys, I downloaded some raw RNA-seq data from GEO, but they came in the bedgraph format with the counts. I would like to transform that bedgraph into gene counts to analyze in DESeq2. Does anyone know how to do this? chr1 14322 14350 2.34 chr1 14350 14351 3.51 chr1 14351 14358 4.6 ...
bedgraph gene counts counts written 13 months ago by LuisNagano40 • updated 13 months ago by gocougs20

Latest awards to LuisNagano

Popular Question 5 months ago, created a question with more than 1,000 views. For How to export rld (rlog) or vsd values from DESeq2?
Popular Question 6 months ago, created a question with more than 1,000 views. For How to export the output list of csCluster( ) from CummeRbund?
Popular Question 13 months ago, created a question with more than 1,000 views. For How can I select my Chip-seq genes (targets) in my Rna-seq data?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For How to get Ensembl ids in cuffdiff output?

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