User: dharl
dharl • 70
- 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
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... 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
dharl • 70
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... 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.
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written 5.2 years ago by
dharl • 70
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... 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 ...
written 5.2 years ago by
dharl • 70
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... 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 ...
written 5.4 years ago by
dharl • 70
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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
dharl • 70
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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
******** ...
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... 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
dharl • 70
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... 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 ...
written 5.5 years ago by
dharl • 70
• updated
4.4 years ago by
marwa.cs91 • 30
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... 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.
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written 5.5 years ago by
dharl • 70
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... Ya I checked for outliers... I think I will ask the mailing group as you have suggested.
...
written 5.5 years ago by
dharl • 70
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