User: Pin.Bioinf
Pin.Bioinf • 220
- Reputation:
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Im a Health Engineer with a Bioinformatics specialization doing epigenetics research.
Posts by Pin.Bioinf
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... Yes, I agree. I was using default parameters, which were "complete" and "euclidean". I tried euclidean with ward.D2 and still, the differentiation between tumor and controls is not clear, it is a blur in the middle of both, and some tumors are the same color as controls as in my original heatmap. ...
written 8 days ago by
Pin.Bioinf • 220
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... I tried with :
hclustfun = function(x) hclust(x,method = 'centroid'),
distfun = function(x) dist(x,method = 'maximum'),
and here is the heatmap I got: seems much better, should I stick with this one?
![Heatmap with different hclust and dist methods][1]
[1]: https://i.imgur.com/RbEFzPS ...
written 8 days ago by
Pin.Bioinf • 220
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... Thanks a lot, kevin!
For scaling, I tried many ways and got the same for all:
-Converting to M values and then using parameter scale='row';
-Using scale='row' on b values;
-Using scale='none' but scaling before the heatmap.
All look similar, so I think I did it correctly. I will check on distance ...
written 8 days ago by
Pin.Bioinf • 220
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... Hello, I am looking at this heatmap and I do not understand why some of the tumours are grouped with the controls, seems as if the heatmap is 'moved to the left':
Top of the heatmap:
![Top of the heatmap][1]
(it is a long heatmap so i upload just a section)
Bottom of the heatmap:
![Bottom of the ...
written 8 days ago by
Pin.Bioinf • 220
• updated
8 days ago by
Kevin Blighe ♦ 35k
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... Thank you so much for your help Kevin, I finally managed to use plink assoc to do the test, and this time I did it for 16 samples: 8 control and 8 case. (just for testing). This is what I got:
CHR SNP BP A1 C_A C_U A2 CHISQ P OR SE L95 U95
1 . 27022976 A 1 1 G 0 1 1 2 0.01984 50.4
1 . ...
written 25 days ago by
Pin.Bioinf • 220
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... I get the error in which says 'Error: --indiv-sort file does not contain all loaded sample IDs.'
here is what my vcf looks like:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample1.bam Sample2.bam Sample3.bam Sample4.bam Sample5.bam Sample20.bam... Sample25.bam ... Sample30.bam
Also, after I ...
written 26 days ago by
Pin.Bioinf • 220
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... Thanks a lot. Am I correct to think MySampleListing.list should be like:
0 Sample1
0 Sample2
..
..
0 Sample15
..
0 Sample30
?
And how about the FAM file? ( only have phenotype (condition) information, but I put it in the FAMILY ID
Family ID Individual ID Paterna ...
written 27 days ago by
Pin.Bioinf • 220
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... Hello, I want to do an association test with plink.
I have two vcf files: one has all common variants for case population, the other has all common variants for control population. I want to feed these vcfs to plink. I don't understand the input plink needs for --assoc command. Is there any way I c ...
written 27 days ago by
Pin.Bioinf • 220
• updated
27 days ago by
Kevin Blighe ♦ 35k
0
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... Thank you! This seems like a nice approach, and what I was looking for.
Would the mydata input be the merged 15samplescase.vcf and 15samplescontrol.vcf ?
And those vcf merged should contain only the common variations among each of the 15 samples ?
Thank you ...
written 4 weeks ago by
Pin.Bioinf • 220
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... Hello,
I have 15 vcf files for one type of population and 15 vcf files for another type. I want to check the differences between the two, and also the similarities. What changes from one group to another and what remains the same, and a signifcance score if possible.
I have read about PLINK but I ...
written 4 weeks ago by
Pin.Bioinf • 220
• updated
4 weeks ago by
Raony Guimarães • 950
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