User: niu.shengyong

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Posts by niu.shengyong

<prev • 53 results • page 1 of 6 • next >
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Interpret contribution of regions in Partitioning heritability enrichment result
... I'm using LDSC tool for working on partitioned heritability enrichment analysis across different cell types. I'm curious is there any way that I can know what regions of the chromosomes contribute in the enrichment scores most? If not, is there any other tool can work for this purpose? Thanks! ...
ldsc enrichment snp ld written 15 months ago by niu.shengyong60
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Comment: C: MA plot x axis meaning
... Thanks for your explanation! ...
written 15 months ago by niu.shengyong60
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MA plot x axis meaning
... Hi there, I'm new to this analysis area, and I already look into many threads, but still don't understand the meaning of "mean normalized counts" in MA plot. Is it the mean normalized read counts between comparison groups? If so, what's the biological meaning of it, and also with fold change ? Thank ...
rna-seq written 15 months ago by niu.shengyong60 • updated 15 months ago by ATpoint41k
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Comment: C: Analyze normalized illumina microarray data
... Thank you! There are many published microarray data in GEO are in this normalized format. I'm curious how did you guys work on that? Thanks ...
written 16 months ago by niu.shengyong60
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Comment: C: Analyze normalized illumina microarray data
... Thanks for your help. I've looked into the limma manual, but still don't know how to use this as input by limma package. Could you give me a hint where to start from the codes? Thanks! ...
written 16 months ago by niu.shengyong60
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Analyze normalized illumina microarray data
... Hi there, is there any way to use normalized signal density table from illumina microarray to do analysis? My goal is to get differential expressed genes. I've looked into limma, but not sure how to use such processed data. Example: #ID_REF = #VALUE = Normalized signal intensity ID_RE ...
illumina analysis rna microarray written 16 months ago by niu.shengyong60 • updated 14 months ago by Biostar ♦♦ 20
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Comment: C: Error of SAMSequenceDictionary
... Do you have any suggestion? Thanks ! ...
written 2.5 years ago by niu.shengyong60
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Comment: C: Error of SAMSequenceDictionary
... Yes. I don't have any duplications in my @SQ lines and got the error ...
written 2.5 years ago by niu.shengyong60
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Comment: C: Error of SAMSequenceDictionary
... Where do you see that? I don't have the same two lines like that actually. Thanks! ...
written 2.5 years ago by niu.shengyong60
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Comment: C: Error of SAMSequenceDictionary
... I don't quite understand what is "extraneous @SQ line"? For example, I have @SQ SN:chr3 LN:198022430 and @SQ SN:chr3 LN:160039680. Should I remove both of them? ...
written 2.5 years ago by niu.shengyong60

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