User: rmf

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rmf0
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Posts by rmf

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DEXSeq Count files do not correspond to the flattened annotation file
... Enter your post below.  Please format any code samples that are included in your question. Information about formatting your code can be found on the F.A.Q. page.Enter your post below.  Please format any code samples that are included in your question. Information about formatting your code can be f ...
dexseq R written 9 months ago by rmf0
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Comment: C: RNA-Seq Batch correction negative values
... My thinking was that I would batch correct the raw counts to get corrected raw counts which would be used in DESeq2 along with the model (which would now exclude the corrected batch variable). What kind of counts do you think the correction should be applied on? It cannot be log-cpm, vst, rlog, voom ...
written 9 months ago by rmf0
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Comment: C: RNA-Seq Batch correction negative values
... Ahan. So batch effect correction works only if all the samples in that batch are affected and not partially? By fixing the negative values, I meant to say to make them all positive because counts cannot be negative. And negative counts cannot be used by DGE packages. Anywya, I will try sva. Thanks f ...
written 9 months ago by rmf0
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RNA-Seq Batch correction negative values
... In my bulk RNA-seq dataset, I noticed a few outliers on MDS plot and on further investigation found that these samples originated from one extraction batch (extbatch) 7.  Fig 1: MDS plot showing outliers and that they belong to extbatch 7. Most of the samples from batch 7 and even batch 8 had lo ...
sva combat rna-seq scran batch-effect written 9 months ago by rmf0 • updated 9 months ago by Aaron Lun20k
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Does SC3 correct counts for gene length?
... Hi, I am interesting in clustering my single cell data to identify clusters and then figure out if certain genes differ in expression profiles and then try to link them to developmental stages.  1. So, to be able to compare gene to gene expression, I suppose the expression scores should be correct ...
rna-seq single-cell scater sc3 biclustering written 11 months ago by rmf0 • updated 10 months ago by Vladimir Kiselev130

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