User: komal.rathi

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komal.rathi80
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Posts by komal.rathi

<prev • 27 results • page 1 of 3 • next >
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Comment: C: Mouse genes not mapping to Human orthologs
... Yeah I was confused because MGI reports the human ortholog but Ensembl does not. Anyway, I will report this to the respective institutions and would like to keep this open here until I get an answer from them. ...
written 4 weeks ago by komal.rathi80
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Comment: C: Mouse genes not mapping to Human orthologs
... Oh yeah, that return statement was a typo. I know two returns are not possible. I'll fix that. The question is still what I have asked: why Rpl18 is not getting mapped to RPL18. ...
written 4 weeks ago by komal.rathi80
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Mouse genes not mapping to Human orthologs
... Hi, I am using biomaRt to convert mouse gene symbols to human and vice versa. Here is the code: library(biomaRt) human = useMart("ensembl", dataset = "hsapiens_gene_ensembl") mouse = useMart("ensembl", dataset = "mmusculus_gene_ensembl") convertMouseGeneList <- function(x, ...
biomart written 4 weeks ago by komal.rathi80
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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 21 months ago by komal.rathi80
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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 2.7 years ago by komal.rathi80
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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 2.7 years ago by komal.rathi80 • updated 2.7 years ago by Matthew Ritchie750
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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 2.8 years ago by komal.rathi80
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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 2.8 years ago by komal.rathi80
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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 2.8 years ago by komal.rathi80
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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 2.8 years ago by komal.rathi80

Latest awards to komal.rathi

Great Question 2.2 years ago, created a question with more than 5,000 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
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Adjust column labels in Heatmap.3
Student 2.2 years ago, asked a question with at least 3 up-votes. For Extract sequence from DNAStringSet object
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Extract sequence from DNAStringSet object
Popular Question 3.3 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 3.3 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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