User: Fereshteh

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Fereshteh2.8k
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I am learning everyday

Posts by Fereshteh

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Comment: C: Stuck on calculating principal components
... > OTU.sum <- aggregate(OTU.sum[2:ncol(OTU.sum)], OTU.sum[1], sum) Error in Summary.factor(2L, na.rm = FALSE) : ‘sum’ not meaningful for factors > like so http://uploads.im/gekOU.jpg Thank you, this data containing three locations "IL,TR, RE" & three amplicons "v1 ...
written 5 days ago by Fereshteh2.8k
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Comment: C: Stuck on calculating principal components
... Sorry, if this is my data from bacteria head((OTU[,1:4])) IPC001 IPC002 IPC003 IPC005 Class_Thermobacula NA "0.000031700" "0.000000000" "0.000000000" Class_Anaerolineae NA "0.000000000" "0.000000000" "0.000013100" ...
written 5 days ago by Fereshteh2.8k
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Comment: C: Stuck on calculating principal components
... Thank you vey much for your help ...
written 5 days ago by Fereshteh2.8k
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Comment: C: Stuck on calculating principal components
... Sorry I plotted 18 SNPs within LCT like so https://ibb.co/jxNRNw but in X axis it does not seem if this 1 mb length around this gene ...
written 6 days ago by Fereshteh2.8k
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Comment: C: Stuck on calculating principal components
... Thank you so much, this is whole of my data SNP p.value Neg_logP chr position type gene rs3754689 0.234851075 0.629207447 2 136590746 typed LCT rs9636213 0.24330764 0.613844253 2 136589278 typed LCT rs12988076 0.282377011 0.549170663 2 136569848 typed LCT rs2322660 0.290876656 0 ...
written 6 days ago by Fereshteh2.8k
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Comment: C: Stuck on calculating principal components
... Thank you by K=4 I got four components, you are all right ...
written 6 days ago by Fereshteh2.8k
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Comment: C: Stuck on calculating principal components
... Thank you, I think you right, I don't know how show that. by Regional association plots gives me this error Space required after the Public Identifier SystemLiteral " or ' expected SYSTEM or PUBLIC, the URI is missing Error: 1: Space required after the Public Identifier 2: Syst ...
written 6 days ago by Fereshteh2.8k
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Comment: C: Stuck on calculating principal components
... Sorry, How can I show 1 million bases surrounding a gene that contains my SNPs?? This is my SNP file head(data) SNP p.value Neg_logP chr position type gene 1 rs3754689 0.2348511 0.6292074 2 136590746 typed LCT 2 rs9636213 0.2433076 0.6138443 2 136589278 typed ...
written 7 days ago by Fereshteh2.8k
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Comment: C: Stuck on calculating principal components
... Yes, exactly At least for me biostars is always helpful. Thank you ...
written 13 days ago by Fereshteh2.8k
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Comment: C: Stuck on calculating principal components
... Hello, thanks a lot As I did not have the age of the genotyped individuals, I therefore ignored age and sex as covariates. I used filtered typed SNPs (call rate=0.99, MAF=0.01, both for samples and SNPS) and two principal coordinates of OTUs calculated by Euclidian distance by vegan package to mode ...
written 13 days ago by Fereshteh2.8k

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