User: dharl

gravatar for dharl
dharl70
Reputation:
70
Status:
New User
Location:
India
Last seen:
4 years, 11 months ago
Joined:
5 years, 6 months ago
Email:
l******************@gmail.com

Posts by dharl

<prev • 19 results • page 1 of 2 • next >
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Answer: A: Permutation Based Thresholds For Eqtl Analysis?
... Hi  From what I know, if you have covariates in the model, you need to preserve the coupling between the covariates and the gene expression, so you just scramble the genotype matrix. Of course, in the end it depends on what you are trying to understand, but if the aim is to break the structure betw ...
written 5.1 years ago by dharl70
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Comment: C: Reactome FI constructing interacting network
... Yes, You are precisely correct. And in some sense that is exactly what I am looking for too, but using reactome as my choice of database.    ...
written 5.2 years ago by dharl70
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Reactome FI constructing interacting network
... I am very new to the Reactome database and Cytoscape. I wanted to build a directed human interactome network. I am just going through the tutorials and the plugin and having a and time getting through it... but if any one has already done this, it would be really great of you could share the informa ...
reactome fi written 5.2 years ago by dharl70
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SNP-gene pairs annotation and enrichment
... HI I have a list of significant SNP-gene pairs after using SNOs genotyped on Illumina platform and using gene expression data. I used MatrixeQTL to obtain this. I am kind of stuck as to how to proceed with understanding these results and would like your views on them. I thought i can check the wher ...
snp written 5.4 years ago by dharl70
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Comment: C: .lgen to .ped conversion failing
... Hi,  sorry it was a mistake, it 7 million. I edited the number now. Well I tried doing it per chromosome... and it gave me the same error. maybe I should split it into smaller files.. but i donot know how to combine them  ...
written 5.5 years ago by dharl70
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Comment: C: .lgen to .ped conversion failing
... This is the error I get. yes I run this on 1.9 Reading pedigree information from [ HNPGenotypes.fam ] plink(7973,0xa02711a8) malloc: *** mach_vm_map(size=1048576) failed (error code=3) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug ******** ...
written 5.5 years ago by dharl70 • updated 4 months ago by RamRS26k
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Answer: A: Microarray analysis beadarray with limma gives no differential expression
... Well, turns out, like Sean said, it was lack of differential expression within my samples. Thanks a lot for all your help.  ...
written 5.5 years ago by dharl70
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.lgen to .ped conversion failing
... So I have converted the reprt.txt and map.txt files into .lgen formats. But my conversion from .lgen to bed file keeps failing due to memory issue even though I try to run it chromosome wise.  Here are the first few lines of my files:  DGKH413ADHJW:Plink_working dlekshmi$ head HNPGenotypes.lgen 1 ...
plink snp written 5.5 years ago by dharl70 • updated 4.4 years ago by marwa.cs9130
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p values from robust Z scores
... I was wondering how to calculate p values from a robust Z score. the robust Z score unlike the normal z score is calculated using the median and absolute deviation from median(MAD) instead of the mean and standard deviation. This way, it is not sensitive to outliers. ...
z scores tests statistics written 5.5 years ago by dharl70
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Comment: C: Microarray analysis beadarray with limma gives no differential expression
... Ya I checked for outliers... I think I will ask the mailing group as you have suggested.  ...
written 5.5 years ago by dharl70

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