User: hsu

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hsu0
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Posts by hsu

<prev • 20 results • page 1 of 2 • next >
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Error in pheatmap: formal argument "scale" matched by multiple actual arguments
... Hello I am using *pheatmap* and my code is : pheatmap(RPL_fpkm_data, scale = "row", annotation_col = a, treeheight_row=0, treeheight_col=0, cluster_cols = FALSE, cluster_rows = FALSE,scale = "none", show_colnames=F, color = colorRampPalette(colors = c("bl ...
R pheatmap written 1 day ago by hsu0 • updated 20 hours ago by zx87545.0k
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161
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monocle clustering cells without marker genes error
... I am using monocle to analyse my gene_counts matrix. I am trying to use function :clustering cells without marker genes. And I am following the guideline on the website. My code is : HSMM <- reduceDimension(HSMM, max_components = 2, num_dim = 6, reduction_method = 'tSNE', verbose = T) T ...
R monocle tool rna-seq written 5 weeks ago by hsu0
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Answer: A: Seurat -FindVariableGenes problem
... Make sure you run NormalizeData prior to running FindVariableGenes. Not doing so can cause this error in some cases. I solved this problem by doing so. ...
written 7 weeks ago by hsu0
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Seurat -FindVariableGenes problem
... I am using Seurat to find variable genes , my code is : f <- FindVariableGenes(object = f, mean.function = ExpMean, dispersion.function = LogVMR, x.low.cutoff = 0, x.high.cutoff = 3, y.cutoff = 0.5) And I got this error: Calculating gene means 0% 10 20 30 40 50 60 70 ...
software error seurat findvariablegenes written 7 weeks ago by hsu0
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Comment: C: scimpute problem: error in read table
... I am not using `GeneCounts_3F-A37B12C16D21.csv` file from `scImpute` package. My work is on R-studio. `GeneCounts_3F-A37B12C16D21.csv` is my own gene-counts matrix. I am a little confused about the permission problem. ...
written 7 weeks ago by hsu0
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scimpute problem: error in read table
... I used scImpute to normalize my data in R. code is : scimpute(count_path = system.file("extdata","GeneCounts_3F-A37B12C16D21.csv", package ="scImpute" ), infile="csv", outfile="csv", out_dir="./", labeled = FALSE, drop_thre= 0.4, Kcluster=4, nc ...
rna-seq written 7 weeks ago by hsu0 • updated 7 weeks ago by Ram17k
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Comment: C: SCnorm -plotCountDepth error
... thank you. I solved this problem by your advice ...
written 8 weeks ago by hsu0
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86
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SCnorm -plotCountDepth error
... I am using SCnorm to normalize my gene_counts matrix. I have 107 samples(4 conditions, each has 57, 19, 18, 13 samples) I used these codes to see the count-depth relationship: Conditions = rep(c(1,2,3,4), each= 57, 19, 18, 13) countDeptEst <- plotCountDepth(Data = d, Conditions = Condi ...
rna-seq written 8 weeks ago by hsu0
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148
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5 follow
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perl compilation errors
... I want to extract fpkm information and I used a perl script: more PB_stressed_sample.txt | perl -ne 'BEGIN{my %F;my %G; my $C=0; @S=("gene","genename");}@a=split;push @S,$a[0];open(my $fh, "<", " SRX3084$a[0]/genes.fpkm_tracking");$C++;<$fh>;while (my $row = <$fh>) {@b=spli ...
assembly written 10 weeks ago by hsu0 • updated 10 weeks ago by Michael Dondrup44k
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Comment: C: featureCounts problem annotation
... Thank you very much ...
written 10 weeks ago by hsu0

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