Comments (10)
@knakamura6222053
リプライ見れたらリアクションください!
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すみません!
昨日まで解析が立て込んでいたので、今日一日使って参考にしながら進めようと思っています。
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終わりました!5章に入っていこうかと思います!
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5章の途中進んでいるのですが、メモリエラーが起こってしまいました。
論文に記載してある、QCを変更してより厳しい条件に設定しても難しいですか?
※計算メモリの方が原因で落ちてそうです。
pbmc.data <- Read10X(data.dir = "/Users/idrc/Desktop/singlecell_test/GSE149689/")
pbmc <- CreateSeuratObject(counts = pbmc.data, project = "pbmc3k", min.cells = 3, min.features = 200)
pbmc[["percent.mt"]] <- PercentageFeatureSet(pbmc, pattern = "^MT-")
pbmc <- subset(pbmc, nFeature_RNA >= 200 & nFeature_RNA <= 5000 & percent.mt < 15)
pbmc <- pbmc %>%
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NormalizeData() %>%
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FindVariableFeatures(selection.method = "vst", nfeatures = 2000) %>%
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ScaleData(features = VariableFeatures(object = pbmc)) %>%
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RunPCA() %>%
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RunUMAP(dims = 1:20) %>%
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FindNeighbors(dims = 1:10) %>%
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FindClusters(resolution = 0.5)
Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Centering and scaling data matrix
Error: vector memory exhausted (limit reached?)
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@dogTK
4章のサンプルでも試してみたのですが、同じところでエラーが出てしまいました。
Centering and scaling data matrix
Error: vector memory exhausted (limit reached?)
FindNeighbors(dims = 1:10)
FindCluster(resolution = 0.5)の値を変更してみたのですが、状況は変わりませんでした。
何か改善策はありますでしょうか…
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@dogTK
お忙しい中、ありがとうございます。
他のPCで環境を作り直して私の方でも何かできないか試してみます!
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@knakamura6222053 こちら完了しました?
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あ、いえいえ!自分のペースでやってもらって大丈夫です!
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@knakamura6222053
確認します!
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#4 こっちにつくりなおしたのでクローズ
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Related Issues (5)
- scRNA-seq本 第4章をやる HOT 10
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