User: Abhishek Pratap

gravatar for Abhishek Pratap
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Posts by Abhishek Pratap

<prev • 21 results • page 2 of 3 • next >
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processing Illumina HT12v4.0 expression data from GEO
... Hi Guys I would like to know the basic analysis workflow for downloading and processing a Illumina HTV12 expression data from GEO. I have seen the beadArray vignette but not sure which normalization process to use. For example with Affy datasets I normally download the raw data and normalize it wi ...
normalization affy process geoquery frma written 5.3 years ago by Abhishek Pratap170 • updated 5.2 years ago by Sean Davis21k
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Comment: C: converting probeset id to gene id's : fRMA
... just for completeness I found the following work from Aron et al to be useful. They have looked the the probeset specificity, coverage etc to select an optimal probeset for a gene thereby enabling simple one to one mapping. Jetset: selecting an optimal microarray probe set to represent a gene Qiyua ...
written 5.3 years ago by Abhishek Pratap170
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Comment: C: converting probeset id to gene id's : fRMA
... Thanks everyone specially for replying on the weekend. Cheers! -Abhi On Mon, Jun 23, 2014 at 10:18 AM, Federico Lasa wrote: > Another thing to consider is the platform you are using, it might be > relevant since some Affy chips (i.e. HuGene 1.0 ST) can be summarized > in different ways ( ...
written 5.3 years ago by Abhishek Pratap170
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converting probeset id to gene id's : fRMA
... Hey Guys I am using fRMA to normalize n summarize some affy data. Post normalization I am getting 54k uniq probe id's in the eSet. I am wondering whats the best way to convert this expressionSet into a gene level data. I thought fRMA's documentation said it would produce gene level summarized valu ...
probe affy convert frma written 5.3 years ago by Abhishek Pratap170 • updated 5.3 years ago by Peter Langfelder2.2k
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Comment: C: help with array based microRNA data analysis
... Hi Paul Appreciate your quick response. So in my case what I am looking for is to create a matrix of expression values of these miRNA and in process also filter out any low quality measurement. I am wondering if LIMMA can do just that. The downstream goal is to integrate some of this info with the ...
written 5.8 years ago by Abhishek Pratap170
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help with array based microRNA data analysis
... Hey Guys We have some custom array based microRNA data scanned using GenePix 4000B scanner and stored in gene pix results (gpr file format). In this case it is not necessarily case-control study as all of our samples are actually with the disease. Our plan is to first generate a simple matrix of n ...
limma microrna written 5.8 years ago by Abhishek Pratap170 • updated 5.8 years ago by Paul Geeleher1.3k
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Comment: C: help with analysis of genotyping data from Illumina HumanOmni5-4v1_B chip
... Thanks a lot Stephanie for your quick response. This is was very useful info. I will follow up with package specific questions if any. Cheers! -Abhi On Tue, Jan 14, 2014 at 1:54 PM, Stephanie M. Gogarten wrote: > Hi Abhi, > > 1. The GWASTools package was designed for QC of precalled arra ...
written 5.8 years ago by Abhishek Pratap170
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help with analysis of genotyping data from Illumina HumanOmni5-4v1_B chip
... Hi Guys We have recently obtained from precalled genotype data from our collaborators generated from the Illumina Human Omni5 array chip (HumanOmni5-4v1_B). The genotypes have already been called using the Illumina's Genome Studio. I being new to the array based genotyping data (coming from sequen ...
snp annotation written 5.8 years ago by Abhishek Pratap170 • updated 5.8 years ago by Stephanie M. Gogarten720
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Comment: C: DESeq: help with analysis
... Thanks Lorena and Steve. Using the DeSeq2 I was able to get a list of genes after FDR adjustment. We do some expected functional enrichment there which is great. I would be curious to know the changes in DESeq2 but I guess the paper is not yet out. Cheers! -Abhi On Tue, Oct 15, 2013 at 1:33 PM, ...
written 6.0 years ago by Abhishek Pratap170
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DESeq: help with analysis
... Hi Everyone Given the study design( see below) I am somewhat surprised NOT to see any genes being differentially expressed with p.adj < .05 or .10. I would like the help from folks on this mailing list to introspect the analysis and figure out if we overlooked something or data Study Design: 4 ...
deseq written 6.0 years ago by Abhishek Pratap170 • updated 6.0 years ago by Lorena Pantano100

Latest awards to Abhishek Pratap

Popular Question 3.4 years ago, created a question with more than 1,000 views. For ggvis: interactive heatmaps
Popular Question 3.4 years ago, created a question with more than 1,000 views. For help with analysis of genotyping data from Illumina HumanOmni5-4v1_B chip
Popular Question 3.4 years ago, created a question with more than 1,000 views. For processing Illumina HT12v4.0 expression data from GEO
Popular Question 3.4 years ago, created a question with more than 1,000 views. For WGCNA: help with comparing multiple GEO studies
Popular Question 3.4 years ago, created a question with more than 1,000 views. For converting probeset id to gene id's : fRMA
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Comparing two gff/gtf files : de novo transcripts v/s reference
Popular Question 3.4 years ago, created a question with more than 1,000 views. For ggvis: interactive heatmaps

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