User: elpsakkas

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Posts by elpsakkas

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Comment: C: remove batch effect using limma
... Great! Thanks! ...
written 3.7 years ago by elpsakkas0
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Comment: C: remove batch effect using limma
... Great! It makes sense, i will try this way as well... Could you have a look at the heatmaps? I posted them above.. Appreciate it ...
written 3.7 years ago by elpsakkas0
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Comment: C: remove batch effect using limma
... Hey Steve, Thanks for your reply..this is the original initial heatmap: https://dl.dropboxusercontent.com/u/14753468/p_correlation_all_data_SE.pdf And this is the heatmap after removal of the batch effect: https://dl.dropboxusercontent.com/u/14753468/p_correlation_all_data_SE_corrected.pdf What ...
written 3.7 years ago by elpsakkas0
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Comment: C: remove batch effect using limma
... I think i got it..! Thank you. So, in a few words in the first case (before the batch removal), my scale of correlation values between my samples is approximately 0.2 - 0.4 (for the 90% of the samples). After i remove the batch effect the scale is becoming more than 0.5 (for 90% of the samples). Doe ...
written 3.7 years ago by elpsakkas0 • updated 3.7 years ago by Gordon Smyth39k
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Comment: C: remove batch effect using limma
... Yes you are right...I follow the Deseq2 protocol. This is the code: countsMmus <- cd[ which( geneTypes=="ENSM" ), ] countsERCC <- cd[ which( geneTypes=="ERCC" ), ] sfERCC <- estimateSizeFactorsForMatrix( countsERCC ) sfMmus <- sfERCC nCountsERCC <- t( t(countsERCC) / sfERCC ) nCou ...
written 3.7 years ago by elpsakkas0 • updated 3.7 years ago by Steve Lianoglou12k
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remove batch effect using limma
... I have a quick question concerning the removal of the batch effect using removeBatchEffect()…   I have RNA-seq data and i have three batches. I normalize using spike in RNA and i estimate size factors (following the Deseq methodology). At the end i get a matrix which i log2 transform. When i do PC ...
rnaseq limma batch effect pearsoncorrelation written 3.7 years ago by elpsakkas0 • updated 3.7 years ago by Aaron Lun25k

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Popular Question 3.7 years ago, created a question with more than 1,000 views. For remove batch effect using limma

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