User: Mehmet

gravatar for Mehmet
Mehmet200
Reputation:
200
Status:
Trusted
Location:
Japan
Last seen:
2 hours ago
Joined:
2 years, 10 months ago
Email:
m*********@duzce.edu.tr

Posts by Mehmet

<prev • 213 results • page 1 of 22 • next >
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Comment: C: Getting Error with bowtie2! "Error: Couldn't build bowtie index with err = 1"
... At tophat2 command, try not to write .fa extension ...
written 1 day ago by Mehmet200
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Comment: C: PCA plot of RPKM data from RNA-Seq dataset
... Hi, I am trying to make a PCA plot. I have 17 samples, how can I make it ? plot(pca$rotation[,1],pca$rotation[,2], xlab = "PC1", ylab = "PC2") text(pca$rotation[,1],pca$rotation[,2], row.names(pca$rotation), cex=0.5, pos=4) When I type the codes above, I receive different results. I mean posi ...
written 1 day ago by Mehmet200
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Comment: C: PCA plot from read count matrix from RNA-Seq
... Thank you for help. I do not know variance between PC1 and PC2. When I run commands, I did not get variance value. I have 17 PCs when I type below: Standard deviations: [1] 3.49034964 1.22304723 1.05526472 0.99765777 0.76043084 0.56623044 0.37994839 [8] 0.24585524 0.23052947 0.1 ...
written 1 day ago by Mehmet200
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Comment: C: PCA plot from read count matrix from RNA-Seq
... Sorry, Please have a look https://ibb.co/gWx7Q6 https://ibb.co/cYbCsm ...
written 2 days ago by Mehmet200
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Comment: C: PCA plot from read count matrix from RNA-Seq
... Hi Kevin, I have uploaded two figures. my commands: project.pca <- prcomp(t(MyReadCountMatrix)) project.pca.proportionvariances <- ((project.pca$sdev^2) / (sum(project.pca$sdev^2)))*100 barplot(project.pca.proportionvariances, cex.names=1, xlab=paste("Principal compon ...
written 2 days ago by Mehmet200 • updated 2 days ago by genomax37k
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Comment: C: PCA plot from read count matrix from RNA-Seq
... Hi Kevin, Thank you very much. Should I do anything in my FPKM data prior to PCA plot? I have run analyses to generate PCA plot (pairs plots). I would like to ask you a few things: 1. What are the dots in boxes? 2.What are the numbers around each boxes? I have 17 samples in my data, but I have 15 ...
written 2 days ago by Mehmet200
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Comment: C: PCA plot from read count matrix from RNA-Seq
... Hi Kevin, I guess we obtain reads counts from HtSeq, and performed DEG analyses using edgeR. I have 23 samples. Previously, I generated a PCA plot using read.count.matrix data following your codes above. I also would like to ask you; what is difference between generating a PCA plot from PC1 to PC5 ...
written 3 days ago by Mehmet200
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Comment: C: PCA plot from read count matrix from RNA-Seq
... Hi Kevin, I also want to perform a PCA plot. I have a read-count matrix data. You mentioned that we need to normalize data prior to PCA plot. Could you please help me how to normalize the data? ...
written 3 days ago by Mehmet200
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Comment: C: Possible evolutionary studies using whole genome and RNA-seq data
... Hi, Good suggestion. Thank you. 1. Phylogenomics based on ortholog proteins from genome and/or transcriptome data. 2.Gene family evolution (insertions/deletions, expansion of gene families) from genome and/or transcriptome data. ...
written 10 days ago by Mehmet200
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Comment: C: Goat Genome gene prediction
... You can select the first and second scaffolds of your genome and load them to Artemis. The first and second scaffolds are the biggest ones in your genome. My concerns are to make sure about your gene sets, as your downstream analyses absolutely depend on good gene sets.This is why I want you to get ...
written 11 days ago by Mehmet200

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