Closed camilafarias112 closed 3 years ago
Hello Camila!
Can you please share the whole fData(exp)
table? The problem I suspect is that the column .type
contains one or more NA's.
Another thing that I need to debug this is to know if your description
file contains a column named type
.
Thank you, Xavier.
Hello Xavier,
Here you go my fData(exp)
:
> fData(exp)
Family .fct .trn .std .imp .type
ACKR1 receptor numeric
ACKR2 receptor numeric
ACKR3 receptor numeric
ACKR4 receptor numeric
B cell cell numeric
B cell memory cell numeric
B cell naive cell numeric
B cell plasma cell numeric
Cancer associated fibroblast cell numeric
CCL1 chemokine numeric
CCL11 chemokine numeric
CCL13 chemokine numeric
CCL14 chemokine numeric
CCL15 chemokine numeric
CCL16 chemokine numeric
CCL17 chemokine numeric
CCL18 chemokine numeric
CCL19 chemokine numeric
CCL2 chemokine numeric
CCL20 chemokine numeric
CCL21 chemokine numeric
CCL22 chemokine numeric
CCL23 chemokine numeric
CCL24 chemokine numeric
CCL25 chemokine numeric
CCL26 chemokine numeric
CCL27 chemokine numeric
CCL28 chemokine numeric
CCL3 chemokine numeric
CCL3L1 chemokine numeric
CCL3L3 chemokine numeric
CCL4 chemokine numeric
CCL4L2 chemokine numeric
CCL5 chemokine numeric
CCL7 chemokine numeric
CCL8 chemokine numeric
CCR1 receptor numeric
CCR10 receptor numeric
CCR2 receptor numeric
CCR3 receptor numeric
CCR4 receptor numeric
CCR5 receptor numeric
CCR6 receptor numeric
CCR7 receptor numeric
CCR8 receptor numeric
CCR9 receptor numeric
CCRL2 receptor numeric
Class-switched memory B cell cell numeric
Common lymphoid progenitor cell numeric
Common myeloid progenitor cell numeric
CX3CL1 chemokine numeric
CX3CR1 receptor numeric
CXCL1 chemokine numeric
CXCL10 chemokine numeric
CXCL11 chemokine numeric
CXCL12 chemokine numeric
CXCL13 chemokine numeric
CXCL14 chemokine numeric
CXCL16 chemokine numeric
CXCL17 chemokine numeric
CXCL2 chemokine numeric
CXCL3 chemokine numeric
CXCL5 chemokine numeric
CXCL6 chemokine numeric
CXCL8 chemokine numeric
CXCL9 chemokine numeric
CXCR1 receptor numeric
CXCR2 receptor numeric
CXCR3 receptor numeric
CXCR4 receptor numeric
CXCR5 receptor numeric
CXCR6 receptor numeric
Endothelial cell cell numeric
Eosinophil cell numeric
FPR1 receptor numeric
GPR75 receptor numeric
Granulocyte-monocyte progenitor cell numeric
Hematopoietic stem cell cell numeric
HRH4 receptor numeric
immune score cell numeric
Macrophage cell numeric
Macrophage M1 cell numeric
Macrophage M2 cell numeric
Mast cell cell numeric
microenvironment score cell numeric
Monocyte cell numeric
Myeloid dendritic cell cell numeric
Myeloid dendritic cell activated cell numeric
Neutrophil cell numeric
NK cell cell numeric
PF4 chemokine numeric
PF4V1 chemokine numeric
PITPNM3 receptor numeric
Plasmacytoid dendritic cell cell numeric
PPBP chemokine numeric
stroma score cell numeric
T cell CD4+ (non-regulatory) cell numeric
T cell CD4+ central memory cell numeric
T cell CD4+ effector memory cell numeric
T cell CD4+ memory cell numeric
T cell CD4+ naive cell numeric
T cell CD4+ Th1 cell numeric
T cell CD4+ Th2 cell numeric
T cell CD8+ cell numeric
T cell CD8+ central memory cell numeric
T cell CD8+ effector memory cell numeric
T cell CD8+ naive cell numeric
T cell gamma delta cell numeric
T cell NK cell numeric
T cell regulatory (Tregs) cell numeric
XCL1 chemokine numeric
XCL2 chemokine numeric
XCR1 receptor numeric
Sending also attached the tableMissing(exp), if that helps...
And my description
object only has one column called family
Thank you so much for your attention!
Camila
I have exposure names with spaces... do you think that would impact anything? Like "B cells"...
@camilafarias112 Yes, having names with spaces yields to errors indeed! I might need to add a block on the read function to make sure this is not an issue anymore. Can you please use exposure names without spaces and report back the results?
Thanks in advance, Xavier.
Hello @ESCRI11 - the normality test is running! :D
After some tests, the issue was not the spaces alone. +
,-
,)
and (
in the exposure
list gave me the error. When I replaced all of them for _
I moved forward in the workflow.
I appreciate very much the attention, can't way to see the results from rexposome
!
All the best and take care, Camila
Thanks for the feedback @camilafarias112 . I will look into it to be sure this is no longer a problem in the future. I will include this update on a future version (to be determined).
Hello developers,
First I'd like to let you know that the idea of this workflow is just perfect for what I work with and I look forward to be able to use it in regular basis!
I started to follow the workflow, but I faced an error message when checking normality in this data. Would you guys help me with that?
`> head(sampleNames(exp)) [1] "CL29085" "CL29118" "CL29137" "CL29150" "CL29151" "CL29159"
Since my exposure object is a matrix, numeric, why the normality processing is not running? Thank you so much,
Camila