User: mms140130

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mms14013050
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Posts by mms140130

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Why there is 2 copy numbers for same patients for the same gene?
... I have the CNV downloaded from TCGA2STAT in R, for BRCA patients. The data looks as follows: gene TCGA-3C-AAAU TCGA-3C-AAAU A1BG 0.1302 0.0064 A2M 0.2586 0.0033 A2MP1 0.2586 0.0033 NAT1 0.2662 0.0034 The same patient has 2 different CNV values for the same gene, why? ...
cnv written 8 months ago by mms14013050 • updated 8 months ago by Emily_Ensembl15k
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Comment: C: covert the file to .ped file
... yes I use MAC,anyway I solved the .map issue ...
written 10 months ago by mms14013050
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Comment: C: covert the file to .ped file
... yes I'm trying to do association ...
written 10 months ago by mms14013050
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Comment: C: covert the file to .ped file
... I think the ped file is not complete as you said I don't know why? I followed your coding but still having this issue ...
written 10 months ago by mms14013050
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Comment: C: covert the file to .ped file
... after i solved the issue of .map, I got the following error A problem with line 1 in [ plinkv2.raw ] Expecting 2 + 2 * 199 = 400 columns, but found 392 what should I do here? ...
written 10 months ago by mms14013050
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Comment: C: covert the file to .ped file
... Thank you for your help but when I apply the following code to my data it gives me empty file head -1 plink.raw | sed 's/ \+/\n/g' | sed '1,2d' | awk '{print "0\t"$0"\t0\t0"}' > plink.map ...
written 10 months ago by mms14013050
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Comment: C: covert the file to .ped file
... it gave me the following error No file [data1pr3.fam] exists ...
written 10 months ago by mms14013050
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covert the file to .ped file
... I have the following data ID Affection rs3117294 rs2747453 rs2747454 rs2747457 rs3131888 D0024949 0 C_C A_G A_G A_A A_G D0024302 0 A_C A_A A_G A_A A_A D0023151 0 C_C A_G A_A A_A G_G D0022042 0 A_C A_A G_G A_A A_A D0021275 0 C_C A_G A_G A_A A_G D0021163 0 A_A A_A G_G A_A ...
R written 10 months ago by mms14013050 • updated 10 months ago by Kevin Blighe28k
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Comment: C: Methylation data duplicated for same gene
... For The A2ML1 I have cg27653134 and cg03490200 for A4GALT they are cg07393322 and cg09744051 ...
written 10 months ago by mms14013050
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Methylation data duplicated for same gene
... Hi, I downloaded Methylation data using package TCGA2STAT in R as follows methyl<- getTCGA(disease="BRCA", data.type="Methylation", type="27K") it has two outputs the methyl$dat which has the data head(methyl$dat[,1:3]) TCGA-01-0628-11A-01D-0383-05 TCGA-01-0630-11A-01D- ...
gene R written 11 months ago by mms14013050

Latest awards to mms140130

Popular Question 9 months ago, created a question with more than 1,000 views. For plot the rows of dataset in R
Centurion 11 months ago, created 100 posts.
Supporter 14 months ago, voted at least 25 times.

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