User: rishi.dasroy

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rishi.dasroy10
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New User
Location:
Finland
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6 months, 3 weeks ago
Joined:
2 years, 11 months ago
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r***********@gmail.com

Posts by rishi.dasroy

<prev • 7 results • page 1 of 1 • next >
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How to get genes corresponding to a GO term from topGOData object?
... Hi, I have a topGOdata object which is built with following command > GOdata <- new("topGOdata", description = "Simple session", ontology = "BP", allGenes = na.omit(t), geneSel = topDiffGenes, nodeSize = 10, annot = annFUN.gene2 ...
microarray topgo gene ontology R written 20 months ago by rishi.dasroy10 • updated 4 months ago by mt10220
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Comment: C: How to use brainarray custom cdf with any bioconductor package?
... I was trying to normalize 64 CEL files with a single command and the system was not responding (with 8 cores and 16 gb RAM, it was running for 56 hours ) . But I still found the resultant file given in "outFilePath". Now I understand the process may not be able to save all the exons in the file. Ac ...
written 2.6 years ago by rishi.dasroy10
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Answer: A: How to use brainarray custom cdf with any bioconductor package?
... Stephen , Thank you so much for quick response. But I normalized them with exonArrayTarget="probeset" parameter. I have also checked the number of exons defined in the brainarray cdf. It is 337485 which is more than what I am getting from the SCAN.UPC   > t <-as.data.frame(table(moex10stm ...
written 2.6 years ago by rishi.dasroy10
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Comment: C: How to use brainarray custom cdf with any bioconductor package?
... Yes I have used Brainarray gene and exon mappings both for fiRMA and SCAN.UPC. I have received same number of genes by both the method but it is different in case of exons.   ...
written 2.6 years ago by rishi.dasroy10
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Comment: C: How to use brainarray custom cdf with any bioconductor package?
... Hi James, Thanks for your response. I have normalized the exons through SCAN.UPC package using  moex10st_Mm_ENSE.cdf to check alternative splicing . Although there are 337485 exons in this cdf , but after normalization with SCAN.UPC I have only got normalization value of 228057 exons. However norm ...
written 2.6 years ago by rishi.dasroy10
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Comment: C: How to use brainarray custom cdf with any bioconductor package?
... Hi Steve, Thanks for your answer. I have visited SCAN.UPC page and it looks promising. Can you explain and provide examples more how to do DE of gene and exons using this? Thanks rishi ...
written 2.9 years ago by rishi.dasroy10
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How to use brainarray custom cdf with any bioconductor package?
... I am trying to analyse affymetrix exon array with latest relaease of brainarray custom cdf. I have tried 'affy' package with follwing command > Data <- ReadAffy(cdfname ='moex10stmmrefseqcdf') Error: The affy package is not designed for this array type. Please use either the oligo or xps p ...
customcdf affy oligo written 3.0 years ago by rishi.dasroy10

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Popular Question 19 months ago, created a question with more than 1,000 views. For How to use brainarray custom cdf with any bioconductor package?

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