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Recent Replies
Comment: Differences between published differential gene expression results and own analy
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ATpoint
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Please link the paper, lets see their methods. With human data it can well be that they included something like surrogate variables to damp…
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dsull
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There are many ways to do normalization and one of the correct ways is simply to plug raw counts into deseq2 (the math that deseq2 uses to …
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Is it the version number in your data?
e.g. ENST00000415118.1 vs ENST00000415118 could be causing the mismatch?
Comment: Differences between published differential gene expression results and own analy
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So is there any correct way for normalisation? I know limma recommends CPM via limma-voom and DESeq2 just takes in raw counts and does thei…
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Thanks a lot for your answer. I will check the paper.
Comment: Differences between published differential gene expression results and own analy
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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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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.
The largest difference will come from the post-processing & analysi…
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I second the comment about comparing the top 100 genes - if you see vastly different results, I would lean closer to examining protocols th…
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I think what you are asking involves too much work for anyone to explain it in granular detail. But who knows, maybe there is a good soul o…
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