For data (syn3157329), it has 1709 individuals in total.
In file "AMP-AD_ROSMAP_Rush-Broad_AffymetrixGenechip6_Imputed_chr1.dosage.gz" (syn5879161), it has 1709 dosage values; while in file "AMP-AD_ROSMAP_Rush-Broad_AffymetrixGenechip6_Imputed.fam" (syn5879839), it has 1708 rows in total, why are they not the same? Thanks.
Created by xinxingwu Hi, thanks for your kind reply. Thanks for the useful information. I got it. Now I can use specimenID=> individualID=> projid to relate them.
Thank you for your help. Hi there, in answer to your questions:
1. Yes, the "id" column in syn5879839 corresponds to the study + the projid. If you remove the "ROS" or "MAP" characters from those strings, you will be able to map them to the projid column in the ROSMAP clinical metadata file.
2. The corresponding fam file for the imputed CHOP samples is here: syn7769936. We are working on making that connection between the files more explicit in the AD portal; for now we have a link in the SNP Array methods description but it's easy to miss.
Hope that helps -- let me know if you have any other questions!
Thanks. I also tried chr22. I got it. Actually, chr1 also has 1711 columns. Thanks for your help.
In addition,
1)the second column in the file "AMP-AD_ROSMAP_Rush-Broad_AffymetrixGenechip6_Imputed.fam" (syn5879839), could it be regarded as the sample IDs, that is, Study+ projid? Could I use it to correlate Metadata by this second column in syn5879839? For example, using the second column in syn5879839 to correlate ROSMAP_clinical.csv (syn3191087)?
2)for "ROSMAP imputed dosage chop_Illumina "(syn2426141), is there a corresponding fam file? Since the number of columns (about 385 columns) in syn2426141 is much smaller than the number of columns in "AMP-AD_ROSMAP_Rush-Broad_AffymetrixGenechip6_Imputed.fam" (syn5879839)?
Thanks. I didn't try chr1, but chr22 has 1711 columns, the first 3 of which are marker annotations. Thus, it has 1708 dosages. How many columns are you seeing for chr 1?
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