User: komal.rathi

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komal.rathi40
Reputation:
40
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New User
Location:
United States
Last seen:
2 months, 3 weeks ago
Joined:
2 years, 3 months ago
Email:
k**********@gmail.com

Posts by komal.rathi

<prev • 24 results • page 1 of 3 • next >
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DEXSeq - Error in estimateSizeFactorsForMatrix(featureCounts(object)
... Hi everyone, I have exonic counts for 344 samples for 15 genes that include some house-keeping genes like GAPDH and Actin genes using dexseq_count. I am trying to normalize them like this: dxd = DEXSeqDataSetFromHTSeq( countFiles, sampleData = sampleTable, design= ~ sample + exon + disease_ ...
dexseq dexseq_count dexseqdatasetfromhtseq written 4 months ago by komal.rathi40
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Comment: C: CRLMM: Which array type work with which annotation package
... Thanks for the response. A documentation on the columns required in the custom annotation would be really helpful as well.  ...
written 16 months ago by komal.rathi40
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CRLMM: Which array type work with which annotation package
... Disclaimer: Crossposted on Biostars. I am using the CRLMM package. We have about 21000 IDATs that belong to the following array types: Array Annotation Package (Guess) HumanHap550 human550v3b Human610-Quad human610quadv1b HumanOmniExpress-24v1-1 Not sur ...
crlmm written 16 months ago by komal.rathi40 • updated 16 months ago by Matthew Ritchie690
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Comment: C: Voom: need at least two non-NA values to interpolate
... That was a typo - removed FPKM from my question. Thanks! ...
written 17 months ago by komal.rathi40
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Comment: C: Voom: need at least two non-NA values to interpolate
... The 8000 observations are broken down by tissue type and I compare each tissue type with every other. So there could be 5 replicates in one tissue type and 1000 in other. The biggest concern I have is if I can really voom the expected counts that I have for RSEM or not. ...
written 17 months ago by komal.rathi40
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Comment: C: Voom: need at least two non-NA values to interpolate
... I am trying to use voom on expected counts (not FPKM) from RSEM. ...
written 17 months ago by komal.rathi40
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Comment: C: Voom: need at least two non-NA values to interpolate
... Yes. I cannot have all the genes in one matrix because I am facing a memory issue: I have ~60000 rows and 8000 columns if get all the data and process it. Can I not use voom on expected counts (not FPKM) from RSEM?  ...
written 17 months ago by komal.rathi40
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Voom: need at least two non-NA values to interpolate
... Hi, I am trying to apply voom to expected counts from RSEM (I don't have raw counts). My next step is to compute a differential test using limma. # matrix I am trying to apply voom to has 1 row and 8021 columns: > dim(tmp) [1] 1 8021 # first five columns > tmp[,1:5] ...
voom fpkm limma voom rsem written 17 months ago by komal.rathi40
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CRLMM: Error in quantile.default(M, c(1, 5)/6, names = FALSE)
... Hi everyone, I am working with crlmm package for the chip BDCHP-1X10-HUMANHAP550_11218540_C. The following is my code: library(Biobase) library(crlmm) library(VanillaICE) library(lattice) library(ff) library(illuminaio) library("human550v3bCrlmm") library("human610quadv1bCrlmm") cnSet <- geno ...
crlmm written 18 months ago by komal.rathi40 • updated 8 months ago by Matthew Ritchie690
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Answer: A: CRLMM: the leading minor of order 1 is not positive definite
... There were discrepancies in the chip types for some of the IDATs. Correcting that resolved the issue. ...
written 18 months ago by komal.rathi40

Latest awards to komal.rathi

Popular Question 23 months ago, created a question with more than 1,000 views. For DESeq and Limma+Voom Normalization for Rna-Seq Data Using Ercc Spike-In
Popular Question 23 months ago, created a question with more than 1,000 views. For Extract sequence from DNAStringSet object
Scholar 23 months ago, created an answer that has been accepted. For A: CRLMM: the leading minor of order 1 is not positive definite

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