User: rmf

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rmf10
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Posts by rmf

<prev • 8 results • page 1 of 1 • next >
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batchelor batch correction correction runs into errors
... I am trying to use batch correction using the [batchelor](https://bioconductor.org/packages/release/bioc/html/batchelor.html) package on two **bulk** RNA-Seq datasets . But, I run into errors. ```r > batchelor::fastMNN(as.matrix(dc),as.matrix(de)) more singular values/vectors requested than avai ...
rna-seq mnncorrect fastmnn batchelor batch-correction written 11 weeks ago by rmf10
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Best normalisation method
... I have Infinium methylation EPIC data. I am experimenting with different normalisation to figure out which is the best. All samples come from the same tissue which is blood. Two metrics that I thought would be useful are variance between samples for each probe and sample to sample correlation. ![en ...
microarray epigenetics minfi epic methylationepic written 8 months ago by rmf10
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Beta values and M values cluster differently
... I have an Infinium methylationEPIC dataset that I use R package **minfi** to analyse. I normalized (noob, swan, func, quantile)(sex info used for func and quantile) the data and convert to beta values. XY probes are now removed. Beta values for autosomal probes are then converted to M values. MDS ...
microarray epigenetics minfi epic methylationepic written 8 months ago by rmf10
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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 2.1 years ago by rmf10
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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 2.1 years ago by rmf10
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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 2.1 years ago by rmf10
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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 2.1 years ago by rmf10 • updated 2.1 years ago by Aaron Lun25k
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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 2.2 years ago by rmf10 • updated 2.2 years ago by Vladimir Kiselev150

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Popular Question 2.1 years ago, created a question with more than 1,000 views. For RNA-Seq Batch correction negative values

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