User: komal.rathi

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komal.rathi40
Reputation:
40
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New User
Location:
United States
Last seen:
5 months, 3 weeks ago
Joined:
2 years, 6 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 7 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 19 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 19 months ago by komal.rathi40 • updated 19 months ago by Matthew Ritchie730
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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 20 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 20 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 20 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 20 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 20 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 21 months ago by komal.rathi40 • updated 11 months ago by Matthew Ritchie730
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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 22 months ago by komal.rathi40

Latest awards to komal.rathi

Great Question 14 months ago, created a question with more than 5,000 views. For Extract sequence from DNAStringSet object
Popular Question 14 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 14 months ago, created a question with more than 1,000 views. For Adjust column labels in Heatmap.3
Student 14 months ago, asked a question with at least 3 up-votes. For Extract sequence from DNAStringSet object
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Extract sequence from DNAStringSet object
Popular Question 2.2 years ago, created a question with more than 1,000 views. For DESeq and Limma+Voom Normalization for Rna-Seq Data Using Ercc Spike-In
Scholar 2.2 years 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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