User: carleshf

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carleshf10
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Spain/Barcelona/ISGlobal
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2 months, 1 week ago
Joined:
2 years, 8 months ago
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Posts by carleshf

<prev • 7 results • page 1 of 1 • next >
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Bach effect and PEER/RUV correction on large population
... Dear all,   We are working with a large population with more than 1200 samples. From those samples, we got both gene expression and methylation data using Affymetrix HTA 2.0 and Illumina 450k. Both data were pre-processed using Affymetrix Expresion Control (GCCN-SST-RMA normalization pipeline) and ...
sva methylation batch effect ruv gene expression written 11 months ago by carleshf10
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Answer: A: miRNA normalization for large amount of samples using LVSmiRNA
... The last version of the package allows to include a "subsample" to the estVC function. For example: MIR.RA <- estVC(MIR, subsample=sample(1:50)) With this, computational time is reduced. ...
written 11 months ago by carleshf10
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miRNA normalization for large amount of samples using LVSmiRNA
... Dear all, I'm trying to use LVSmiRNA to normalize a total of ~1700 (agilent) samples. The problem is that the step when estVC is called takes lot of time. The vignette of the package propose to use multicore package but this packages is deprecated and CRAN suggest to use parallel. Hence I just ch ...
mirna normalization written 13 months ago by carleshf10
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DESeq2 log2FoldChange of 48?
... Dear all, I used DESeq2 to perform a DE analysis on mRNA and, when extracting the contrasts I found that one of them has strange values on log2FoldChange. Examples of this values are: baseMean log2FoldChange lfcSE stat pvalue padj control.norm control.norm.sd case.norm ...
deseq2 written 2.1 years ago by carleshf10 • updated 2.1 years ago by Wolfgang Huber13k
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DESeq2 :: correction by donor when donor corresponds in block with another variable
... Dear all, I am performing a differential expressed genes analysis using DESeq2 and I want to correct the design by donor and by season (winter vs. summer where the extraction was done). The problem is that the the donor corresponds with the season in sets. An example of data is: id time ...
deseq2 deggenes written 2.4 years ago by carleshf10 • updated 2.4 years ago by Michael Love15k
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CellMix - Custom matrix with Abbas signature
... Dear all,   I'm using the package CellMix to deconvolute an expression matrix. What I'm doing is call directly the function gedBlood with my expression matrix, like this: res <- gedBlood(e, verbose=TRUE) But I get this error: Loading basis signature from Abbas et al. (2009) ... OK ...
deconvolution cellmix written 2.5 years ago by carleshf10
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Deconvolution RNA-Seq data
... Dear all, I am working with human blood samples in a DE genes analysis. Now we want to perform the deconvolution of the matrix of counts to see the different cell types. My idea is to follow the guidelines described here, here and here but with RNA-seq data. I found that the R package DeconRNASeq c ...
differential expression rna-seq written 2.7 years ago by carleshf10 • updated 2.7 years ago by James W. MacDonald45k

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