User: jjrin

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jjrin10
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Posts by jjrin

<prev • 34 results • page 1 of 4 • next >
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Comment: C: Prefiltering gene lists and DESeq
... Thanks for your reply! The problem is that my gene lists are already prefiltered because I did batch correction on them (using sva seq) which requires prefiltering. Therefore all of my gene lists are different lengths since I batch corrected them in subsets, one treatment with one master control gr ...
written 8 months ago by jjrin10
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Prefiltering gene lists and DESeq
... Hello, I am doing DESeq on my RNA-Seq data. However, I have filtered my conditions individually based on the replicates within each condition. Basically, I have 5 conditions with 5 replicates. I filtered each condition based on the rowmeans of the replicates (5 and above reads are kept). However, no ...
R deseq rna-seq written 8 months ago by jjrin10 • updated 8 months ago by h.mon22k
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Comment: C: R ggplot Align Y-Axis on multiple graphs
... Oh my you're right, I use the same username there and I thought I was posting there. Won't do that again. ...
written 9 months ago by jjrin10
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R ggplot Align Y-Axis on multiple graphs
... Hello I used ggarrange to create this plot, and I would like to align the y axis so that the y axis is the same throughout all graphs instead of being off center. Thank you. ![Misaligned y axis][1] [1]: https://image.ibb.co/k3s6YH/image.png ...
R ggplot2 ggarrange written 9 months ago by jjrin10 • updated 9 months ago by Kevin Blighe33k
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Can't make sva comparison despite very distinct batch effects
... I continuously receive this error when I try to run sva with my count data R code for sva: # Loading all variables library(sva) dat <- dds_matrix idx <- rowMeans(dat) > 1 dat <- dat[idx,] mod <- model.matrix(~batch, colData(dds)) mod0 <- model.mat ...
sva factors batch effect written 10 months ago by jjrin10
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Plotting a PCA Plot from SVASeq results
... Hello, I used SVASeq to remove batch effects in my data set. I have run SVASeq and gotten 8 surrogate variables and all of the covariates necessary for my conditions. How would I plot a more detailed PCA plot rather than the give plot svseq function that is used in the vignette? I am thinking of s ...
pca plot sva batch effects svaseq ruvseq written 10 months ago by jjrin10
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Using Mann-Whitney U Test to compare replicates
... Hello, I have several replicates of a certain variable (at least 5). I would like to compare these distributions to see how similar they are with each other. I have TPMs as a measurement as well as counts (if necessary). They are not normally distributed and I read that the Mann-Whitney U-Test is an ...
R rna-seq statistics written 13 months ago by jjrin10 • updated 13 months ago by Jean-Karim Heriche17k
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Salmon, Getting New TPM from new, updated NumReads
... Hello, I have recently normalized my read counts (NumReads in Salmon output) and I would like to get the new updated TPMs using these Numreads counts. Is there a method I could go around doing this? The effective length and length would be the same regardless. I have all of the same data available, ...
numreads alignment salmon written 13 months ago by jjrin10
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Comment: C: Salmon never completes, stuck on processing fragments
... Yes, it's fine for now, I have been running all of my programs with this many threads and i am currently not multithreading. ...
written 15 months ago by jjrin10
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Salmon never completes, stuck on processing fragments
... Hello I have been running salmon on some single-ended data. It runs fine initially and does process fragments, however it never actually completes. Here is my command history /usr/local/bin/Salmon-0.8.2_macOX_10.12/bin/salmon quant -p 24 -i /Volumes/RNA_SEQ/Reference_Genomes/Index/XENLA_JGIv1 ...
fastq salmon rna-seq written 15 months ago by jjrin10

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