User: komal.rathi
komal.rathi • 40
- Reputation:
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- Location:
- United States
- Last seen:
- 5 months, 3 weeks ago
- Joined:
- 2 years, 6 months ago
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Posts by komal.rathi
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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 7 months ago by
komal.rathi • 40
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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 19 months ago by
komal.rathi • 40
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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 19 months ago by
komal.rathi • 40
• updated 19 months ago by
Matthew Ritchie • 730
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... That was a typo - removed FPKM from my question. Thanks!
...
written 20 months ago by
komal.rathi • 40
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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 20 months ago by
komal.rathi • 40
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... I am trying to use voom on expected counts (not FPKM) from RSEM.
...
written 20 months ago by
komal.rathi • 40
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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 20 months ago by
komal.rathi • 40
5
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... 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]
...
written 20 months ago by
komal.rathi • 40
0
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1
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400
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1
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... 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 ...
written 21 months ago by
komal.rathi • 40
• updated 11 months ago by
Matthew Ritchie • 730
0
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1
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401
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... There were discrepancies in the chip types for some of the IDATs. Correcting that resolved the issue.
...
written 22 months ago by
komal.rathi • 40
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