User: mohammedtoufiq91
mohammedtoufiq91 • 110
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Posts by mohammedtoufiq91
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... Hi @rpolicastro , thank you very much. ...
written 4 hours ago by
mohammedtoufiq91 • 110
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... Hi @rpolicastro, thank you very much for the inputs.
Another question, I wanted to know if there is a way to draw horizontal lines over the Boxplot to indicate or label the p-value significance values as represented in the example plot or this should be manually created.
 in ggplot2. Could you please assist me how to do the same or provide any useful resources.
dput(head(Data))
...
written 1 day ago by
mohammedtoufiq91 • 110
• updated
1 day ago by
rpolicastro • 710
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... Thank you for the comments @Kevin Blighe. ...
written 8 weeks ago by
mohammedtoufiq91 • 110
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... Thank you for the inputs @Kevin Blighe. I will look the annotations for the yellow samples that grouped at the top.
Regarding this, `Evidence against there being a batch effect is illustrated by many blue and yellow samples grouping together`, if the samples are grouped that means it has batch effe ...
written 8 weeks ago by
mohammedtoufiq91 • 110
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... Hi,
I have a question about batch effect. I used the qRT-PCR transcript targeted assay with around 300 genes with 160 samples (included 30 samples from batch 1 and 130 samples from batch 2). Batch 1 experiment and Batch 2 experiment was performed on different days. I used normalized log2-scale rela ...
written 8 weeks ago by
mohammedtoufiq91 • 110
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... @RamRS, please find the data below:
head(Neg_Dct_v1)
S1_1 S1_2 S1_3 S1_4 S1_5 S1_6
Batch "Batch_1" "Batch_1" "Batch_1" "Batch_2" "Batch_2" "Batch_2"
Plate "Plate_1" "Plate_2" "Plate_1" "Plate_2" " ...
written 8 weeks ago by
mohammedtoufiq91 • 110
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... @ATpoint and RamRS, thank you for the reply. The solution provided here is PCA on sample level. However, I am looking to plot PCA on genes and label them by Batch and Plate information. Genes on rows and samples on columns. Basically see cluster formation of genes on PCA with Batch and Plate level i ...
written 8 weeks ago by
mohammedtoufiq91 • 110
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... Hi,
I have a question about plotting PCA on genes, I have samples in rows with associated annotations (Batch and Plate information) and genes in the columns. I have performed PCA on samples and I am familiar with it. However, I am interested to plot PCA on genes now and color by batch and plate inf ...
written 8 weeks ago by
mohammedtoufiq91 • 110
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... Thank you very much @Prakash. ...
written 9 weeks ago by
mohammedtoufiq91 • 110
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