User: mathavanbioinfo

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Posts by mathavanbioinfo

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single probe represent multiple genes?
... Hello friends I am doing micro array data analysis(HGU1333plus2), i got the expression matrix file by using gcrma , but the some probe is represent multiple gene like this . how can we treat this, then some probe is not matched it shows NA can delete it , next i take this file for analyze  WGCNA , ...
microarray gcrma expressionset written 2.7 years ago by mathavanbioinfo10 • updated 2.7 years ago by svlachavas740
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How to combine multiple probes representing a single gene?
... Hello friends I am doing micro-array data analysis using the Affymetrix data  ,then i created the expression matrix,  now the  file contain multiple probe representing the single genes, Can any one share your knowledge on R script to merge the probes Id or any related articles. Best Regards Matha ...
microarray affy eset written 2.7 years ago by mathavanbioinfo10 • updated 2.7 years ago by Gordon Smyth38k
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WGCNA analysis with NCBI GEO Series Matrix file?
... Hello all, I am trying to find co expression module of different viruses Using WGCNA package, Can  any one tell me how to use "NCBI GEO SOFT files for co expression analysis.That contain probe list with the expression value of sample, duplicate probes are existing.So kindly  share your valuable ide ...
wgcna geo data written 2.8 years ago by mathavanbioinfo10 • updated 2.8 years ago by Peter Langfelder2.2k
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Comment: C: What are all the different methods available for identifying the DEG?
... Thank you for your reply, Can u send me R Code(limma) ...
written 2.8 years ago by mathavanbioinfo10
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What are all the different methods available for identifying the DEG?
... Dear All,  I am working on Micro-array data analysis  with this GEO acc no. GSE31747, In this paper PMID 22024983 (https://www.ncbi.nlm.nih.gov/pubmed/22028943) they have used ANOVA method to identify the significant genes,Now i am  trying to compare their results with Limma package but i am not ge ...
microarray limma written 2.8 years ago by mathavanbioinfo10 • updated 2.8 years ago by Gordon Smyth38k
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Row and column design for Micro-array data data analysis?
... Hello  I am trying to DEG by Limma with R i got error message , can any one help me > fit = lmFit(celfiles.gcrma, design) Error in lmFit(celfiles.gcrma, design) :    row dimension of design doesn't match column dimension of data object   ...
limma written 2.8 years ago by mathavanbioinfo10 • updated 2.8 years ago by Gordon Smyth38k
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Virus NGS data analysis?
... Hello Every one I am a Research Scholar, doing analysis on  "The Understanding of Virus Pathogenesis" through Host-virus interaction, I want to use Publicly available NGS data. Can any one please suggest me, can i go with this topic for my PhD work,Your comments are welcome Best Regards Mathavan ...
genomics written 2.8 years ago by mathavanbioinfo10
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Limma and DEG
... hi I am using LIMMA to identify DEGs. I got the top 5 DEGs. But i am not able to get the whole list of DEGs with proper id and genes.  Here i used the code  write.table(topTable(fit, coef=1, adjust="fdr", sort.by="B", number=500), file="limma_complete.xls", row.names=F, sep="\t")   ...
limma written 2.9 years ago by mathavanbioinfo10 • updated 2.9 years ago by Aaron Lun25k

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Popular Question 2.5 years ago, created a question with more than 1,000 views. For How to combine multiple probes representing a single gene?

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