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mani2012 / BatchQC

Provides Quality Control of sequencing samples by deducing if there is batch effect and adjusts for it.
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PCA plot tooltips show incorrect values with ComBat and SVA #12

Closed meono closed 5 years ago

meono commented 5 years ago

Hi,

I noticed the tooltips on PCA plot show incorrect values for chosen PCs when ComBat or SVA adjusted data is selected: (EDIT: I just realized that the tooltip shows the PCs from None adjusted data even when ComBat or SVA is selected.)

image

This was generated with an example data but I get the same issue with my own data.

library(BatchQC)
data(example_batchqc_data)
batch <- batch_indicator$V1
condition <- batch_indicator$V2
batchQC(signature_data, batch=batch, condition=condition)

I'm using BatchQC_1.8.0 and can send a full session info if you can't replicate it.

(just a personal preference: A tooltip that shows "condition" in stead of "PCs" might be more helpful when there are numerous conditions.)

Also, thanks a lot for this tool.

mani2012 commented 5 years ago

Hi,

Thanks for bringing this to notice. I just fixed it. The fix should be available in the next build in a day or two.

Thanks, Mani

From: Emre Özdemir notifications@github.com Sent: Thursday, September 20, 2018 4:30 AM To: mani2012/BatchQC BatchQC@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [mani2012/BatchQC] PCA plot tooltips show incorrect values with ComBat and SVA (#12)

Hi,

I noticed the tooltips on PCA plot show incorrect values for chosen PCs when ComBat or SVA adjusted data is selected:

[image]https://user-images.githubusercontent.com/8055398/45804432-5aeaa200-bcbc-11e8-83fe-c255f63766a3.png

This was generated with an example data but I get the same issue with my own data.

library(BatchQC)

data(example_batchqc_data)

batch <- batch_indicator$V1

condition <- batch_indicator$V2

batchQC(signature_data, batch=batch, condition=condition)

I'm using BatchQC_1.8.0 and can send a full session info if you can't replicate it.

(just a personal preference: A tooltip that shows "condition" in stead of "PCs" might be more helpful when there are numerous conditions.)

Also, thanks a lot for this tool.

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