zhangyuqing ComBat-seq issues

zhangyuqing / ComBat-seq

Batch effect adjustment based on negative binomial regression for RNA sequencing count data

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issues

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Can i nordmalise without having commvon sample between two repeats

#43 ucbtsh6 opened 3 months ago
0
The covariates are confounded

#42 SimonSchlumbohm opened 3 months ago
3
Batch effect present for some biotypes after running CombatSeq

#41 kvn95ss opened 5 months ago
0
no data rows with required number of counts

#40 Chenjlin28 opened 7 months ago
0
A strange problem

#39 zonzero opened 10 months ago
1
Plus one (well, I mean more than one) samples

#38 woodyNsinbad opened 10 months ago
0
ComBat-seq doesn't support 1 sample per batch yet

#37 jianwu1 opened 1 year ago
0
Combat-seq, Pseudoaligners and DESeq2

#36 pintoa1-mskcc opened 1 year ago
0
running combat-seq with DESeq2

#35 Mercilena opened 1 year ago
0
scRNAseq - CombatSeq

#34 SalimMegat closed 1 year ago
0
How to adjust by multiple variables using ComBat-Seq?

#33 evaesquinas opened 1 year ago
3
Error in order(y) : unimplemented type 'list' in 'orderVector1'

#32 dea-jenaer opened 2 years ago
0
Common not tagwise dispersion used when one level of covariate - Code error?

#31 reidbm opened 2 years ago
0
Keep getting the error that rows do not match

#30 sameet-sema4 opened 2 years ago
1
ComBat_seq took a very long time

#29 rongwong1119 opened 2 years ago
11
Can I Use ComBat-Seq to adjust multigroups RNAseq?

#28 yirenheihei opened 2 years ago
0
Using ComBat-Seq to adjust for batch effect/ colony ID

#27 mastoldt opened 3 years ago
0
Multiple corrections

#26 tea-radut opened 3 years ago
0
Error in qr.default(design) : NA/NaN/Inf in foreign function call (arg 1)

#25 chiwwong opened 3 years ago
3
Run combat-seq on continues variable

#24 jeppeseverens opened 3 years ago
0
Using ComBat-Seq over RSEM estimated counts

#23 ali-kishk opened 3 years ago
1
different output after changing group parameter

#22 mikagm opened 3 years ago
0
the vignette returns a matrix | array, real data returns a list

#21 AGordonRobertson opened 3 years ago
1
ComBat-Seq correction creating very large count values--cannot feed into DESeq2

#20 cdharshika opened 3 years ago
10
Implementation with DESeq2 > "invalid class “DESeqDataSet” object: the count data is not in integer mode"

#19 samuellup opened 3 years ago
5
ComBat-seq + DESeq2 / WGCNA Or DESeq2 (batch as covariate) / ComBat + WGCNA

#18 sharvarinarendra opened 3 years ago
9
Error in .compressOffsets(y, lib.size = lib.size, offset = offset) : offsets must be finite values

#17 maximinio opened 3 years ago
1
install issue on R4.02 and R4.03

#16 sundaochun opened 3 years ago
0
combat-seq produces very large values after batch adjustment for some genes

#15 marykthompson opened 3 years ago
1
support for multiple cpus?

#14 cjhong opened 3 years ago
0
combat-seq can set a reference batch like combat?

#13 taojinsheng closed 3 years ago
1
ComBat-Seq and pseudobulk counts

#12 AmelZulji closed 3 years ago
2
Install error

#11 zckoo007 closed 3 years ago
1
readcount to FPKM

#10 alibumizj closed 3 years ago
2
ComBat (negative value) and ComBat_seq (lib-size)

#9 bio-zs closed 3 years ago
4
including more than one feature to be corrected

#8 leonorrib closed 3 years ago
1
ComBat-seq + DESeq2

#7 14lwt1 closed 3 years ago
4
Error in phi_matrix

#6 JOUNGCHANGYOUNG closed 3 years ago
6
ComBat_seq cannot be found

#5 Zepeng-Mu closed 3 years ago
11
bug in getting adjusted counts matrix

#4 davidroad closed 3 years ago
8
Question concerning further analysis

#3 JJBio closed 3 years ago
3
Working with normalized datasets

#2 tengfei-emory closed 4 years ago
2
Genes reduced after ComBat-seq

#1 SL1993 closed 4 years ago
1