User: llo

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llo0
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Posts by llo

<prev • 7 results • page 1 of 1 • next >
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Outputting batch-effect free normalized counts
... Hello, I have used the RUVg function in RUVSeq to successfully remove the batch effects in my two groups of samples. Both are controls so I am not concerned about removing any biological significance or signal of interest. I have created RLE and PCA plots that have the demonstrated the desired effec ...
edaseq ruvseq svaseq written 18 days ago by llo0 • updated 17 days ago by davide risso520
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Comment: C: Batch effects between controls
... Thank you, I completely missed 2.4, it does exactly what I need it to   ...
written 24 days ago by llo0
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Comment: C: Batch effects between controls
... Ah, I meant that all the data sets I got off SRA was at the same stage, used the same sequencer, were from the same species, and had the same preparation (poly A selection). However, these two data sets was either single or pair ended. Since I specifically chose controls, I thought that each data se ...
written 24 days ago by llo0
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Comment: C: Batch effects between controls
... Thank you for your reply. I will try using negative control genes but the vignette does not include how to use specific genes but rather how to use spike ins. I have a list of potential control genes but no spike ins, do you know how to use a list of genes that I have by gene name to use as a negati ...
written 24 days ago by llo0
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Batch effects between controls
... Hello, I am working with data that I downloaded from the SRA database. I am only working with the same stage, library preparation, and species. However, when I plot a PCA plot of the data, they do not align very well even though I am using the same reference genome and annotation. How would I correc ...
ruvseq batch-effect written 24 days ago by llo0 • updated 24 days ago by James W. MacDonald45k
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Pairwise comparison using DEXSeq and interpreting results
... Hello, I am interested in doing a pairwise condition with DEXSeq, I have read your earlier answer here: https://support.bioconductor.org/p/74354/#98534, but I am still confused as to how to implement it. How would I subset the DEXSeqDataSet? I have 2 conditions, 3 replicates each, and 3 stages. Over ...
dexseq plotdexseq written 4 months ago by llo0
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Comment: C: Pairwise comparasion for multiple conditions using DEXSeq
... Hello, I am also interested in doing a pairwise condition with DEXSeq. How would I subset the DEXSeqDataSet? I have 2 conditions, 3 replicates each, and 3 stages. Overall, 18 different samples. My data set looks like this:          condition stage GFP_18_1       GFP    18 GFP_18_2       GFP    18 ...
written 4 months ago by llo0

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