ComBat-seq

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I am currently working on an RNA-Seq dataset with an unbalanced design and two factors: treatment and colony ID (I am working with social insects, so colony ID is important...

mastoldt

I have an RNA experiement with 2 factors, and one is confounding with the batch effect. Running ComBat seq on my data, with a formula of ComBat_seq(count_matrix, batch=batch, group =...

tea-radut

Error in qr.default(design) : NA/NaN/Inf in foreign function call (arg 1)

3

I encountered the error when I ran the following: `ComBat_seq(cts, batch = coldata_filtered$Rep2, group=NULL, covar_mod=cbind(coldata_filtered$Cancer, coldata_filtered$Treatment))` `Error in qr.default(design) : NA/NaN/Inf in foreign function call (arg 1)` I did a...

chiwwong

Hello, I was wondering if it would be possible to run Combat-seq with a continues variable as batch, for example age of patients. Or else, would it be possible to...

jeppeseverens

Hi! I have a very different output every time I try to specify the biological variable using the “group” parameter of ComBat. We have RNA sequencing results from two different...

mikagm

the vignette returns a matrix | array, real data returns a list

1

I've resolved the issue, but will post this brief note anyway on the chance that it might be helpful. In R v4.0.3, with sva v3.36.0, if I run the ComBat_seq...

AGordonRobertson

Error in .compressOffsets(y, lib.size = lib.size, offset = offset) : offsets must be finite values

1

Hi there, I previously used the sva::ComBat function and it worked perfectly: ``` adjusted

maximinio

Error: Failed to install 'sva' from GitHub: (converted from warning) installation of package ‘C:/Users/AppData/Local/Temp/Rtmp6rciWQ/filef5220635c4627/sva_3.35.2.tar.gz’ had non-zero exit status

sundaochun

combat-seq produces very large values after batch adjustment for some genes

1

Hi, I am trying out Combat-seq as a way to reduce batch effects in a dataset prior to use with downstream packages that do not support direct modeling of batch...

marykthompson

I use kallisto output files and trim some features but still, many genes remain. For instance, my input count matrix is 91,897 x 32. ComBat-Seq runs for 2+ days. It...

cjhong