## User: rmf

rmf10
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10
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1 month, 1 week ago
Joined:
2 years, 3 months ago
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r***************@gmail.com

#### Posts by rmf

<prev • 8 results • page 1 of 1 • next >
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... 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 ...
written 11 weeks ago by rmf10
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... 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 ...
written 8 months ago by rmf10
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... 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 ...
written 8 months ago by rmf10
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written 2.1 years ago by rmf10
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... 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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... 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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... 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 ...
written 2.1 years ago by rmf10 • updated 2.1 years ago by Aaron Lun25k
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... 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 ...
written 2.2 years ago by rmf10 • updated 2.2 years ago by Vladimir Kiselev150

#### Latest awards to rmf

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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