User: komal.rathi
komal.rathi • 80
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Posts by komal.rathi
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... 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.rathi • 80
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... 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.rathi • 80
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... 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, ...
written 4 weeks ago by
komal.rathi • 80
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... 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_ ...
written 21 months ago by
komal.rathi • 80
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... 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.rathi • 80
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... 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 ...
written 2.7 years ago by
komal.rathi • 80
• updated
2.7 years ago by
Matthew Ritchie • 750
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... That was a typo - removed FPKM from my question. Thanks!
...
written 2.8 years ago by
komal.rathi • 80
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... 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.rathi • 80
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2.8k
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... I am trying to use voom on expected counts (not FPKM) from RSEM.
...
written 2.8 years ago by
komal.rathi • 80
0
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2.8k
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... 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.rathi • 80
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