User: mbk0asis

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mbk0asis550
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Korea, Republic Of
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Posts by mbk0asis

<prev • 158 results • page 1 of 16 • next >
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WGCNA - consensus analysis - cutreeStatic - no samples selected
... Hello! I'm currently trying to identify consensus gene sets between two different tissue types, Muscle/PBMC, using WGCNA. I have two normalized count matrices from DESeq2 for each tissue type. I simply transposed them and made a list as written in the tutorial. > nSets = 2; > ...
wgcna rna-seq written 14 days ago by mbk0asis550
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Comment: C: Odd DESeq2 results
... After carefully checking the data, I found that I got different normalized count values depending on the samples. I have 36 samples in 5 groups as follow (for simplicity, I changed the sample names to more easily distinguish them), HD_old_1 HD_old_2 HD_old_3 HD_old_4 HD_old_5 ...
written 28 days ago by mbk0asis550
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Comment: C: Seurat3 DimPlot inconsistency
... Thank you, António! I will do that~~ ...
written 4 weeks ago by mbk0asis550
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Seurat3 DimPlot inconsistency
... Hi, all! I'm currently analysing a single cell RNA-seq data using Seurat3. While analysing, I found that the UMAP/tSNE plots by `DimPlot` kept changing everytime I ran it even though I sat the `seed.use` for `RunPCA` and `RunUMAP`. The code I used is below. >nDim = 50 >mipsc <- ...
seurat3 rna-seq seurat written 4 weeks ago by mbk0asis550
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Comment: C: Odd DESeq2 results
... OK. Thank you for spending time for me! I'll check the codes and data again to see if there's any mistakes. ...
written 4 weeks ago by mbk0asis550
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Comment: C: Odd DESeq2 results
... Actual data have more samples in complex conditions, I might have made a mistake copying and pasting the data. Sorry! For clarity, I'm posting the actual values in my DESeq2 data. I still see the strangely too low pvalues. > res[grep("Actc1", rownames(res)),] log2 fold change (MLE): co ...
written 4 weeks ago by mbk0asis550
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Comment: C: Odd DESeq2 results
... Thank you, ATpoint! But I got error with your command. counts(dds[grep("Actc1"), rownames(dds),]) Error in grep("Actc1") : argument "x" is missing, with no default I found a typo in the code, counts(dds[grep("Actc1", rownames(dds)),]) Sample1 Sample2 Sample3 Sample4 Sample5 Sampl ...
written 4 weeks ago by mbk0asis550
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Comment: C: WGCNA heatmap error
... Maybe because you have more modules than colors? Try to increase the values in 'greenWhiteRed()'. ...
written 4 weeks ago by mbk0asis550
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Odd DESeq2 results
... Hi, all! During differential expression analysis using DESeq2, I found odd results from it; some of genes with many missing data were detected as significant DEGs with very low pvalues as follow. log2FoldChange pvalue padj Sample1 Sample2 Sample3 Sample4 Sample5 Sample6 Control1 Control2 ...
deseq2 rna-seq written 4 weeks ago by mbk0asis550
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Comment: C: biomaRt::getSequence - Invalid type argument
... Thank you, RamRS! You are right the list in the vignette doesn't match to actual values. Where did you find the actual type values? ...
written 5 weeks ago by mbk0asis550

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