User: Abhishek Pratap

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Posts by Abhishek Pratap

<prev • 16 results • page 1 of 2 • next >
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Comment: C: crlmm : copy number and genotyping of Illumina data
... Hi Matt congrats on the new publication.. Unfortunately I am not able to run using 10, 20 arrays. The errors this time are more consistent. Let me upload a subset of this data and send the information to you offline. Cheers! -Abhi Instantiate CNSet container.Initializing container for genotyping ...
written 5.2 years ago by Abhishek Pratap160
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Comment: C: crlmm : copy number and genotyping of Illumina data
... aah I seee. let me do that and get back to you guys. Cheers! -Abhi On Thu, Jun 5, 2014 at 10:59 PM, Matt Ritchie wrote: > Hi Abhi, > > The issue is likely to do with your small (n=3) samples size (less than 8 > and our new method, which uses k-means - > http://www.biomedcentral.c ...
written 5.2 years ago by Abhishek Pratap160
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Comment: C: crlmm : copy number and genotyping of Illumina data
... Hey Matt Here is the most recent error I got Instantiate CNSet container.Initializing container for genotyping and copy number estimationProcessing sample stratum 1 of 1Quantile normalizing 3 arrays, one at a time. |===================================================================== =========== ...
written 5.2 years ago by Abhishek Pratap160
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Comment: C: crlmm : copy number and genotyping of Illumina data
... Here it is. hopefully the formatting is not that bad -A > sessionInfo()R version 3.1.0 (2014-04-10) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=C LC_COLLATE=C [5] LC_MONETARY=C LC_MESSAGES=C LC_PAPER=C LC_NAME=C [9 ...
written 5.2 years ago by Abhishek Pratap160
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help with analysis of genotyping data from Illumina HumanOmni5-4v1_B chip
... Hi Stephanie Just wondering if your group has some experience with doing CNV analysis on the same genotyping data. I have the raw idat files and tried crlmm package but unfortunately it failed. I have emailed the developers and waiting for hear back from them. In the interim I was wondering if I c ...
snp variantannotation annotation probe gwastools written 5.2 years ago by Abhishek Pratap160 • updated 5.2 years ago by Stephanie M. Gogarten670
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crlmm : copy number and genotyping of Illumina data
... Hi Matt As it happens this got on the back burner earlier and I am getting back to it now. I am getting similar errors trying to do the CNV analysis on Illumina Omni5 idat files. I would be more than happy to share subset of data with you. Just wondering if you would have time now to help with thi ...
snp annotation normalization crlmm copynumber written 5.2 years ago by Abhishek Pratap160 • updated 5.2 years ago by Matthew Ritchie750
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crlmm : copy number and genotyping of Illumina data
... Hi All I am trying to use crlmm package for doing the genotyping and CNV analysis on a set ~200 samples genotyped on Illumina Omni5 array. I tried following the vignette (seems a bit dated) and got some errors(see below) http://www.bioconductor.org/packages/release/bioc/vignettes/crlmm/inst /doc ...
snp annotation normalization crlmm copynumber written 5.5 years ago by Abhishek Pratap160 • updated 5.5 years ago by Matthew Ritchie750
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Comment: C: beadarray: mRNA QC help
... Just dropping in a gentle reminder if my last update was missed over the weekend. -Abhi On Fri, Jan 24, 2014 at 3:10 PM, Abhishek Pratap wrote: > Hi Levi > > Thanks for the quick feedback. I am still following up on few of the > things that you recommended. I checked with the collab a ...
written 5.6 years ago by Abhishek Pratap160
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Comment: C: beadarray: mRNA QC help
... Hi Levi Thanks for the quick feedback. I am still following up on few of the things that you recommended. I checked with the collab and these were not FFPE specimens. Also I did a quick signal to noise ratio calculation (95% / 5% intensity quantiles ). I am attaching the plot. May be that indicates ...
written 5.6 years ago by Abhishek Pratap160
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beadarray: mRNA QC help
... Hi All I am trying to analyze some mRNA illumina bead level data through bead array. Based on the detection p-values(plot attached): if I read it right significant # probes have no expression which concerns me but I could have easily missed some important step. I am attaching the two box plots 1. ...
probe written 5.6 years ago by Abhishek Pratap160 • updated 5.6 years ago by Levi Waldron80

Latest awards to Abhishek Pratap

Popular Question 5.2 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 5.2 years ago, created a question with more than 1,000 views. For crlmm : copy number and genotyping of Illumina data
Popular Question 5.2 years ago, created a question with more than 1,000 views. For Fwd: summarizeOverlaps behavior on RNA-Seq paired end stranded data
Popular Question 5.2 years ago, created a question with more than 1,000 views. For crlmm : copy number and genotyping of Illumina data

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