User: annkolman78

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Posts by annkolman78

<prev • 12 results • page 1 of 2 • next >
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Comment: C: Correlation plot how to improve?
... Thank you for you answer. I have 2 data sets with the same samples but the RNA was extracted using two different methods. I want to see how they correlate, compare which extraction method is better. Thank you! ...
written 29 days ago by annkolman780
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Correlation plot how to improve?
... Hi, I have 2 RNA sequencing datasets and would like to compare their raw read counts. Their correlation: cor(log(data$set1), log(data$set2)) 0.8734045 cor(data$set1, data$set2) 0.2376726 I have tried to plot them (raw read count and log transformed). I have attached pictures.![l ...
plot correlation written 29 days ago by annkolman780
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Comment: C: How to filter out low read counts
... It is working thank you very much! ...
written 4 weeks ago by annkolman780
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Comment: C: How to filter out low read counts
... Thank you for your answer, I run it and got this error: Error in assay(data)[["exp_count"]] : subscript out of bounds ...
written 4 weeks ago by annkolman780
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Comment: C: How to filter out low read counts
... Hi, Thank you for your reply. I have modified it. What is the reason? But, unfortunatelly it didn't solve the problem. Thank you ...
written 4 weeks ago by annkolman780
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How to filter out low read counts
... Hi, I have my data in a SummarizedExperiment format. I would like to filter out reads that have less than 1 read count (exp_count<1) data data class: RangedSummarizedExperiment dim: 56756 100 metadata(0): assays(10): exp_count TPM ... FPKM ...
summarizedexperiment written 4 weeks ago by annkolman780 • updated 4 weeks ago by Martin Morgan ♦♦ 24k
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Comment: C: how to merge SummarizedExperiment datasets
... Hi Martin, thank you for answering all my questions! As I created a matrix using only 1st assay combined <- cbind(assays(batch1) [[1]], assays(batch2) [[1]]) I also wanted to add clinical info so I run combined_se <-SummarizedExperiment(assays=list(counts=combined), colData=cli ...
written 7 weeks ago by annkolman780
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Comment: C: how to merge SummarizedExperiment datasets
... Thank you for suggestions. As I need data from one assay at the moment I used combined <- cbind(batch1@assay[[1]], batch2@[[1]]) which worked fine and created a matrix object . However, I want to add some clinical information to this matrix. I have a cvs file with a few columns: 1)sampleID ...
written 7 weeks ago by annkolman780
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Comment: C: how to merge SummarizedExperiment datasets
... Thank you for your answer, but unfortunately, I have this error: Error in FUN(X[[i]], ...) : column(s) 'external_gene_source' in ‘mcols’ are duplicated and the data do not match batch1 external_gene_source ENSG0000000000 ...
written 7 weeks ago by annkolman780
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how to merge SummarizedExperiment datasets
... I would like to merge two SummarizedExperiment datasets. Both have the same assays,rownames, row data names but different colnames, colData names. Thank you. batch1 class: RangedSummarizedExperiment dim: 49736 20 metadata(0): assays(13): fpkm posterior_mean_count ... fpkm_ci_uppe ...
summarizedexperiment written 7 weeks ago by annkolman780 • updated 7 weeks ago by Martin Morgan ♦♦ 24k

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