User: mbk0asis

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mbk0asis570
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Korea, Republic Of
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Posts by mbk0asis

<prev • 161 results • page 1 of 17 • next >
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Comment: C: Adding gene set to GSVA
... Great post here! I was looking for exactly the same answer! To get gene sets in ENSEMBL ids, what can I do? Thank you! ...
written 11 weeks ago by mbk0asis570
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Comment: C: GSVA example leukemia returns a 'NULL' object
... Thank you, Kevin! That was exactly the problem here! Apparently, I was following an old tutorial. ...
written 11 weeks ago by mbk0asis570
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GSVA example leukemia returns a 'NULL' object
... Hello! While I tested GSVA using the example dataset, I encountered a problem. Function 'gsva' returned 'NULL', no further analysis could be processed. I just copied the codes form the vignette and ran it as described. I pasted the codes under this question. Could someone help me? Thank you! ...
gsva rna-seq written 11 weeks ago by mbk0asis570 • updated 11 weeks ago by Kevin Blighe66k
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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 3 months ago by mbk0asis570 • updated 12 weeks ago by Biostar ♦♦ 20
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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 3 months ago by mbk0asis570
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Comment: C: Seurat3 DimPlot inconsistency
... Thank you, António! I will do that~~ ...
written 3 months ago by mbk0asis570
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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 3 months ago by mbk0asis570
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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 months ago by mbk0asis570
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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 months ago by mbk0asis570
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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 months ago by mbk0asis570

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