User: Pin.Bioinf

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Pin.Bioinf220
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Malaga
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1 year, 8 months ago
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Im a Health Engineer with a Bioinformatics specialization doing epigenetics research.

Posts by Pin.Bioinf

<prev • 125 results • page 1 of 13 • next >
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Comment: C: Why some tumors are grouped with the controls?
... 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.Bioinf220
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Comment: C: Why some tumors are grouped with the controls?
... 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.Bioinf220
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Comment: C: Why some tumors are grouped with the controls?
... 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.Bioinf220
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Why some tumors are grouped with the controls?
... 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 ...
cpgs methylation written 8 days ago by Pin.Bioinf220 • updated 8 days ago by Kevin Blighe35k
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Comment: C: Different samples order in .ped and phynotype data files
... 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.Bioinf220
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Comment: C: PLINK assoc input: can it be two vcf files case/control?
... 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.Bioinf220
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Comment: C: PLINK assoc input: can it be two vcf files case/control?
... 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.Bioinf220
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PLINK assoc input: can it be two vcf files case/control?
... 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 ...
vcf snps association plink written 27 days ago by Pin.Bioinf220 • updated 27 days ago by Kevin Blighe35k
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Comment: C: Comparing VCF files between two groups (15 vcf files against 15 vcf files)
... 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.Bioinf220
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Comparing VCF files between two groups (15 vcf files against 15 vcf files)
... 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 ...
vcf plink snp variants written 4 weeks ago by Pin.Bioinf220 • updated 4 weeks ago by Raony Guimarães950

Latest awards to Pin.Bioinf

Teacher 1 day ago, created an answer with at least 3 up-votes. For A: STAR --quantMode GeneCounts function
Centurion 11 weeks ago, created 100 posts.
Supporter 4 months ago, voted at least 25 times.
Scholar 4 months ago, created an answer that has been accepted. For A: STAR --quantMode GeneCounts function
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