User: Pankaj Agarwal

gravatar for Pankaj Agarwal
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Posts by Pankaj Agarwal

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Interpreting Spade analysis results
... Hi, I have installed the most recently version of spade and run it successfully with the example data that comes with the package and also with my own CyTOF data.  But I am having a hard time interpreting the results. A huge number of files are generated.  I could not find much information in the v ...
spade written 2.1 years ago by Pankaj Agarwal100
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Answer: A: DESeq2: Paired Test
... Hi, I am trying to use DESeq2 for a set of counts obtained via summerizedOverlaps and have the counts for 4 samples in one file. Earlier I had used DESeq2 with counts from htseq-count, which reports the counts for each samples in a separate file. Now that I have these in one file, is there a metho ...
written 5.1 years ago by Pankaj Agarwal100
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Comment: C: countOverlaps Warnings
... I installed R 3.1.0 and install all the bioconductor packages to try out with the latest version, but for some reason summarizeOverlaps() function is not showing as being available. Below is the message that I get when it comes to running the function followed by the sessionInfo(). Not sure if I a ...
written 5.2 years ago by Pankaj Agarwal100
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Comment: C: countOverlaps Warnings
... Yes, these are p.e reads. I made the changes you suggested as follows, everything else being the same as before: bfl <- BamFileList(samplespath, yieldSize=50000, index=character(), asMates=TRUE) ... countDF_intsectionNotEmpty_042414A <- summarizeOverlaps(eByg, bfl, mode="IntersectionNotEmpty ...
written 5.2 years ago by Pankaj Agarwal100
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Comment: C: countOverlaps Warnings
... Valerie, I used summarizeOverlaps() instead, since it seemed simpler to use. I also used htseq-count to get the counts using the same parameters, but I get very different results. >From what I have read and understood, both should give similar results since the counts should be reported at the ...
written 5.2 years ago by Pankaj Agarwal100
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countOverlaps Warnings
... Hi, I am analyzing a matched pair tumor/normal rna-seq data set. After aligning with bowtie2 against UCSC hg19 index, I am trying to get the counts for each of the samples using the iGenomes UCSC GTF file. I came across the following tutorial which shows different ways to do it in Bioconductor: h ...
written 5.2 years ago by Pankaj Agarwal100 • updated 5.2 years ago by Valerie Obenchain6.7k
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Comment: C: DESeq2: Paired Test
... Hi Michael, I followed the vignette for the section on htseq-count and your suggestion as best as I could and got some results. But I am not sure if I did everything right, so I would really appreciate if you could verify if the following steps is the correct way to analyze this data set: There ar ...
written 5.2 years ago by Pankaj Agarwal100
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TCC::ERROR: Need the design matrix for GLM.
... Hi, I have a rna-seq data consisting of matched tumor/normal samples from two patients. For normalization of the counts I am following the steps in the TCC vignette section "3.3 Normalization of two-group count data without replicates (paired)". The output from the commands are as follows: > ...
differentialexpression normalization cancer edger bayseq deseq ebseq tcc written 5.2 years ago by Pankaj Agarwal100 • updated 5.2 years ago by Jianqiang SUN10
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DESeq2: Paired Test
... Hi, This query is in reference to the following post https://stat.ethz.ch/pipermail/bioconductor/2010-April/032869.html where it was mentioned that "DESeq does not support paired tests (yet)". I have a need for performing rna-seq data analysis with matched tumor/normal pairs of data and was wonder ...
deseq deseq2 written 5.2 years ago by Pankaj Agarwal100

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Great Question 24 months ago, created a question with more than 5,000 views. For DESeq2: Paired Test
Popular Question 3.9 years ago, created a question with more than 1,000 views. For DESeq2: Paired Test

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