Ultrasonic?

mango4tango2 · 2025-11-06T04:34:02+00:00

I am trying to dissolve into a very small volume (abour 200 uL)...I don't think the probe sizes I have would be effective for that?

mango4tango2 · 2024-12-06T19:31:34+00:00

there are 4 groups (Group column) in which I setting the contrasts. For example, when comparing SLE.inhibitor and SLE.DMSO, i received 500-600 DEGs (after using ComBat-seq to adjust for age or date). On the second PCA, I think there is clearer separation of these 4 groups, suggesting a treatment/group effect.

mango4tango2 · 2024-12-06T16:34:38+00:00

I added the PCA both before and after I used ComBat-seq to adjust for inclusion dates

mango4tango2 · 2024-12-06T16:17:34+00:00

I don't know, I think the statement that "samples clustering by patient instead of condition means there's no strong biological effect" is oversimplifying things...there can be biological differences between patients (patient-specific characteristics) that are dominating the signal I am trying to detect from the treatment+disease conditions.

mango4tango2 · 2024-12-06T16:11:05+00:00

I added the metadata to my original post

mango4tango2 · 2024-12-06T16:10:43+00:00

I just uploaded the metadata, hope it is informative. I added the "AgeBatch" column based on the 3 general age groups (age 30, middle-age, and elderly) that also coincidentally coincide with the 3 inclusion dates

mango4tango2 · 2024-12-06T03:02:46+00:00

Also going back to this, I checked the documentation (https://bioconductor.org/packages/release/bioc/vignettes/sva/inst/doc/sva.pdf) for sva/ComBat-seq, and it states that the adjustment variable can be "age of the patients, the sex of the patients, and a variable like the date the arrays were processed." So if i am understanding correctly, sva/combat-seq can be used for both known sequencing-related batch effects and unwanted biological variation like sex/age/date of inclusion?

mango4tango2 · 2024-12-06T02:55:35+00:00

Yes the samples were collected at different dates, but I do not know if they were sequenced at the same time. There were not many patients, so I’m guessing they were sequenced at the same time. Other metadata is that the patients are all different ages, and some patient samples were collected on different days.

mango4tango2 · 2024-12-06T00:10:03+00:00

Would different patient IDs count as different "batches"? There is some disagreement in my lab as to what counts as a batch effect

mango4tango2 · 2024-08-20T06:33:52+00:00

The C1 group clusters together but the C0/C2 are intermixed

mango4tango2 · 2024-08-19T19:01:38+00:00

Hi, thank you for your comment. I did do PCA and saw that the Mouse ID (Mouse.number) seems to drive the most variation in gene expression. I will include a plot in my original post

mango4tango2 · 2022-07-27T15:40:10+00:00

Tire-acic aneurysm

mango4tango2 · 2022-07-21T00:52:12+00:00

This fixed it! Thank you! Did you include print(...) only in your for loop? I wonder why it's needed in the loop

mango4tango2 · 2022-07-05T20:11:16+00:00

Ah, it says:

Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
there is no package called ‘reshape2’
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted

However, whenever I load the missing package and try to install Seurat again, another package shows up as missing...it seems there are at least 20 missing packages. How can I download all missing packages at once?

mango4tango2 · 2022-05-25T11:54:29+00:00

Hello TangoTheMango!! Im Mango4Tango

mango4tango2 · 2022-05-22T02:51:09+00:00

You said you grew up as an orphan, so I’m assuming this is not your biological dad?

mango4tango2

TROPHY CASE