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Recent Replies
Comment: Gene expression equivalent of polygenic risk score ?
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Picasa
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Thanks a lot for your answer. I will check the paper.
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dsull
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If those logFCs are different, then that's a normalization issue.
The logFC is straight forward arithmetic (it's simply dividing mean of […
Comment: Differences between published differential gene expression results and own analy
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vernonlim98
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Thanks both for your input. It got me to look at the published methodologies more closely, and you guys were right. One paper that I was re…
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Yes it does not match at all, and those genes that are common in both analysis results have very different logFC and p values
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I am not sure what you mean by this, but I believe that is what I did. With Trinity, I matched all the paired reads together, so they shoul…
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I don't think something exists out of the box. With variants, we have a 'weight' for each variant on disease risk (obtained through large s…
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write.table(df1, "df1.txt",
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That is good confirmation. Bacl to the error message.
> I don't know how to fix this, given that I already did the trimming steps.
DId yo…
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Honestly, those things shouldn't result in a considerable discrepancy.
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When you say vastly different, what do you mean exactly? Does your top 100 up/down not match theirs at all?
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Have a look at tools like SnpEff or Ensembl VEP. Perhaps your bacterial sp is included.
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Yes, I already made the transcriptome with these tools, and the CD-HIT-EST fasta file is the transcript file that I am using for RSEM. Then…
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Oh, ok. It seems like NCBI stores the files in SRA format (thus needing conversion and database lookups by sra toolkit tools) and EBI store…
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